I am sure that you will get much better answers from others but I can suggest a few things. Shutting off a spillway or any water flow will kill any good bacteria and any algae build up. Also once the water stops moving any thing that has settled will dry and tend to float again. When the water comes on it will flush the system. That could be part of the problem. Depending on your setup there might be alot of build up and there could also be standing water that is stagnating.
You mentioned that you had alot of leaves in the pond but got them all out, what about the rocks in the rapids and water falls. Could there be decaying bits trapped in among the rocks. Do you have any wood anywhere in the pond, a log or stump that is leaching tannins into the water, that would cause the water to discolor. Also if you have peat in the pond or coconut fibre they also are tannins. Maybe a lot of peat could have blown into the pond when you were amending the beds around the pond. I would also think about pollen from nearby trees, my neighbors have a big jack pine that coats my whole yard in pollen for weeks at a time. A flocculant should help to bind the fine particles together to help the filters get them out, if you are able to get extra filtration in the pond when you add it it might help, even just a cheap fountain pump wrapped in old linens in a milk crate, just to add to the gph filtered
There was a thread a while back that explained why algae is more likely to grow on the rocks in falls and rapids, it is basically ideal conditions for algae. I am sure the author will repost it for you, as I can not remember where it was. It sounds like your vegatative filter it just starting up, things should improve once the plants get really going. One thing to remember is that it takes a lot of plants to filter and if the water is moving the are not as effective as still water, the water rushes past and the plants can only feed on what gets trapped. A filter garden is great and I use the idea but if you look at natural wetlands they are huge compared to the actual size of the water way.
In the aquarium world polishing water refers to using something to help filter out microscopic particles that color or cloud the water, carbon, zeolite, and special filter pads are used to make the water sparkle with clarity. I have seen filter pads in some of the pond stores that are carbon based to do that but they are pricey. I do not expect my pond water to be sparkling clear and do not use them so I can not be much help there.
If you have been fighting string algae all winter then I assume you are in a warm climate where the water temp does not drop low enough to kill it off but is low enough that the plants go dormant, they are not actively feeding when they are dormant. You may want to ramp up your mechanical filtration for the winter to help with that. Also doing a very thorough clean in the fall should help. Cut back all the die back on the plants and get all the leaves out.
You may also want to remember the ponds cycle every year so you are going to get a bloom in the spring and possibly in the fall when your plants go dormant and there is suddenly a lot more nutrients in the water. One other idea just popped into my head. Do you use barley, it can leach tannins as well. It helps alot for the spring blooms but it will break down after a while. I tried barley pellets in the filter box last year and it helped with the spring bloom but it did discolor the water a bit and the pellets broke down into a foul sludge after a couple months. I had it in three layers of nylons so it did not get out but I will not try it again as I could see what a mess it could have been.
I hope this has been some help. I think that your main problem is the fine particulate in the pond. If you can get rid of it and figure out where it came from it might solve a lot of your problems. Is there a company around you that builds and maintains ponds. Maybe you could hae them come in to do a really good clean, they will have the pond vacs to clean the bottom. You could also drain it yourself and try a power washer, very very carefully, and start from scratch. Good luck

I apologize for the length of this post but the topic/thread is one that raise numerous points. Please realize that we could discuss this in much greater detail - translation: even more words from this yacky, old guy!!! :-)) But I hope this helps. Im sure others will want to add their viewpoints as well.

"Polished water" has a variety of meanings but in general it means water that has had additional treatment typically to remove things that are difficult to remove. The term can be applied to waste-waters and also be applied to drinking water or even your pond water after it has been treated in some fashion by "simpler" methods. Such things as removal of trace organics, trace nutrients (phosphorous, nitrates, etc.), heavy metals, bacterial counts, turbidity are all things that would be "reduced" in a polished water. But using car wax does not make it polished water!!! (sorry for the pun!). There are many methods of achieving this but they tend not to work that well for pond systems because of the nature of the pond environment to adapt to whatever is happening. For example, a flocculent aid (these can be - but not limited to - very long-chain polymers that are added to the water and attach to particles causing them to clump together) may show very good performance for a week or two but lose itÂs effectiveness over time; the pond may have adapted to it and probably has the bacteria available to consume the polymer or other factors. Using zeolites - usually for ion-exchange or removal of inorganic ions - may work for awhile until the exchange capacity is used up or the surface is covered with bacteria so that exchange canÂt take place. Using activated carbon - NOT to be confused with crushing up a charcoal briquets!!! - provides very small pores and huge internal surfaces for sorption of trace organics; it might help with removing your tannins but the A.C. also loses itÂs effectiveness as the pores become saturated or covered with bacteria. Find the source of your tannins is probably a better approach.

Oxygen transport and use in your pond. First, you need to understand that ANY type of bacteria that you can reasonably think of exists in your pond; itÂs there...count on it. Whether or not itÂs there in abundance or is the dominant type depends on the set of conditions that it likes or doesnÂt like. ThereÂs no such thing as a pond that is totally free of anaerobic bacteria, free of pathogens, etc. You may be lucky and not have a specific pathogen present at some point in time but I usually assume that something will ultimately happen to help introduce it into my pond (those @#$@$ birds!). If you were to attempt to measure "them" - any specific microbial entity or pathogen, etc. - you might not find many of "them" there but count on "them" being there. When the correct conditions arise "they" will out-compete the other bacteria or other micro-organisms and grow exponentially until the conditions are no longer as favorable for continued growth. This could be the result of temperature, nutrients, lack of microbial predators...a host of things. The second point is that anaerobic conditions are very easy to establish. If you have a submerged pot in you pond with say a lily growing in it then you will have anaerobic conditions within that pond specifically within the container. Even if the surrounding water is highly saturated with oxygen the soil will be anaerobic or near anaerobic within as little as 1/4 inch from the soil-water interface. This depends on a number of factors including the organic content in that soil. There will be oxygen in and around the roots of the plant since it will transport oxygen deep into the pot but it will still "stink" if you lift the pot out and dig around in it. If you choose to look into this more then search using terminology such as "pore water chemistry" when you look. The third point is that all bacteria and algae respire or use oxygen and the rate at which they will use it is very temperature dependent. Algae will have a net production of oxygen during the day with sunlight but during the night or while slipping through you biofilter it will be consuming oxygen. The fourth point is that many - but certainly not all! - bacteria tend to grow better when attached to surfaces. So in that sense the liner of your pond is part of your biofilter; the inside of you pipe from the skimmer to the waterfall is part of your biofilter; etc. Bacteria attach and grow. When you turn off the flow through the line they continue to consume oxygen until it is so reduced or depleted that their growth environment is no longer adequate. Remember, any bacteria you can imagine are already there. So as the oxygen level in your pipe drops down to zero other bacteria - anaerobic (and facultative anaerobes) take over with the result that the original bacterial coating sluffs off the surface and compounds such as sulfates are now reduced to hydrogen sulfide as well as the formation of other anaerobic by-products (the "stench" you complained about). The same thing will occur in your bio-filter if you decided to save a bit of electricity and shut it down for the night. Usually the biofilter will stay aerobic only for an hour or so if the water temperatures are in the 60's; itÂs on the order of 10 - 15 minutes if the water is in the 90's or higher! As pointed out by Squirelette even debris captured in a fold in you liner can lead to similar conditions be it for release of tannins or creating of a micro-anaerobic environment. When you then turn on the pump or move water through the line all the sluffed bacteria appear as a batch of turbidity and may or may not stink depending on how long the line was allowed to sit there and accumulate the anaerobic degradation products.

You are mostly correct about where oxygen enters your pond. But there is a bit more to it then that. Oxygen will go into the water wherever air is in touch with the water. The rate at which it will do that is higher the more turbulence you provide (which is why your stream and waterfall help a great deal). But it will also be released into your pond by the algae during the day. It will enter the water over in that quiet little corner away from all the obvious water movement. Once the oxygen is in the water it is carried/moved throughout the water simply by the general turbulence/water movement in the water (sometime add a drop of dye or two and watch how fast it is dispersed in your pond). While diffusion (on the molecular scale) will occur it is a very slow process relative to the mixing that is almost constantly taking place in your pond and is not as much a factor as you might imagine. You may not see the same amount of turbulence throughout your pond but there is some still present. The underlying currents are the result of wind action across the surface, water currents induced by your waterfalls ... and even the occasional eddy from a fish fin! But it is definitely present throughout your pond. Adding an aeration stone at some point will significantly increase the mixing and may help with adding oxygen (although it wonÂt if youÂre already saturated or with 95% or so of saturation).

Finally, the growth of algae on surfaces right after going through your biofilter. Your biofilter is nothing more than a place that provides a lot of surface area for a variety of types of bacteria to attach and grow. While we tend to think of them as being just "nitrifiers" it is actually a complex mix of micro-organisms including but not limited to nitrifiers. Other "critters" are there feeding on critters feeding on bacteria, etc. But the net result is that ammonia and dissolved organic carbon compounds are, for the most part, broken down to carbon dioxide and nitrates (this also has interesting impacts on chloramines but IÂll not get started on that topic here). Phosphorous probably is not removed to any significant extent within your biofilter. So now look at the "growth environment" of the water coming out of the biofilter: it will have some oxygen in it (not all of it was used up), it will have phosphorous in it, it will have carbon dioxide in it, it will have nitrates in it. What or who would LOVE that water??? Algae!!!! Yes, if you put plants in there they will take up some of the nutrients but their removal capabilities will not be 100%. Plus the fact that the moving water transports large quantities of the nutrients past the attached algae further promoting their growth. If you had roaring, raging, class 5 rapids, torrents, etc. cascading over the rocks you wouldnÂt see the string algae because the water would abrade it off before they could grow significantly. But in a nutrient-rich environment the algae are sitting there just thanking you for serving their dinner without them even having to order out!!
---David

And now I come along to sound like a 4th grader. LOL! I love your lessons, David. I just wish I could pass the information along accurately and in a lucid manner. You have no idea of the number of your posts I have copied and printed out. Thank you.
Pondbucket, one thing I haven't found that you did was to see if the discoloration is actually suspended particles or stain. You can do this easily. Scoop up a clear jar full of pond water. Set it aside for a while. Overnight is great. In the morning you will see all of the things that are suspended in the water now layered on the bottom of the jar with possibly a bit of organic debris floating on top. If the water is clear then you have a particulate problem. If the water is tea colored you have a tannin problem and you might still have a particulate problem.
This experiment is separate from David's discussion that includes the oxygen, nutrients and algae problems.
If the problem is due to suspended particles then you probably need a flocculant such as a handful of Bentonite scattered across the pond surface. There are other flocculants, but this one seems to be a favorite on this forum. Quilt batting is helpful.
Tannins that stain the water have to be dealt with through a chemical reaction rather than the physical actions used for particulates. My preferred method is running the water over and through Activated Carbon. As David says, this is not broken chunks of charcoal briquets. Certain molecules in the tannins are collected on any exposed surface of the AC. After a while, the AC has collected all it can and doesn't work any more. I whack the bag several times to break it into smaller pieces that expose new surfaces to the water but eventually it must be replaced if tannins are still evident.
After removing the tannins you must identify the culprit that is producing them, as David pointed out. Most of the time it is leaves, fish poop or other organic materials in the water that are slowly breaking down to form mulm. Rocks on the bottom make this a real problem since it traps the debris. Many times it is in the potting soil. Peat is a very common additive to potting soil and it puts out tannins in large quantities. I worry about using pebbles only in waterlily pots since it does trap a lot of debris. I am experimenting with hydroponic materials this year to see if there is an improvement. Since the material is fairly regular, there is more space for water to flow through.
One thing I point out once in a while is that natural AC is preferable to the compressed pellets, IMO. The process of compression reduces the exposed surface. Some even use an adhesive to bind the bits together which reduces it further.
I look for AC where they carry supplies for African Violets. Sandy

Thanks, Sandy, Squirelette, and Prof David (drh1). We always enjoy your humor, David!

BTW, my pond is in KS near Kansas City where we have cold but not hard winters. I didn't run a pump over the winter and it seemed like the algae really took off coming out of winter. I have no wood or peat in the pond. I think the gunk at the bottom is mainly soils-based stuff from pots or however else things get into a pond.

I really like the Idea of a "Filter Garden" to better my setup. It was suggested here by Squirelette but David has been helping me with my water chemistry and he's told me how companies notoriously oversell the capacities of their bio-filters. So maybe what I'll try is changing my upper pool which is more than 200 gals into a giant filter with garden aquatic plants.

I think that is what everyone is suggesting, more filtration right!?
I like the idea of activated carbon filtering too. David, you seem to think it might work but be hard to maintain? I was reading that a quart of carbon has as much surface area as six football fields! Any truth to that?

I might be able to put the carbon in mesh bags in my skimmer filter and another in my bio-falls. What is the best place?

The trouble with creating the giant Filter Garden is I have all my plants scattered on shelves in the lower pool and I just repotted most of them in the last three weeks IN CLAY/SAND mix soil, not ideal for filter media. AGGG! It will take all my plants maybe twelve to fifteen to fill my upper pool (this doesn't include the ten or so hardy water lilies... I'll just keep those down below in the lower pool and call that the lilly pond.

So CO2: what is the best way to measure this and how relevant is it to pond health and the algae or tannins in the water? I think I have used the Tetra Pond Test Kit correctly and there you can chart CO2 but I wasn't sure if it was meant for just aquariums or aquariums or ponds.

Sandy, I'll try the jar of water test to see what it is. I know that I have about a quarter of an inch light silt on the shelves and bottom of the pools. If I get in and walk around (seldom do this) the particulates there are actually light, large and almost clumpy... hard to describe.

Hi,
CO2 in aquariums does really help with algae, if you have the tank conditions right- lighting, filtration, cleanliness. I use it in my tank. I have a DIY setup using an old pop bottle, but it is used mostly to encourage plant growth in heavily planted tanks. You could try it but I do not think you would see much improvement as it targets submerged plants not roots and lilies aspirate from the surface. If you have ruled out any thing getting into the pond from outside then the particulate is likely to be the dead algae from your spring bloom and whatever had settled into the lines while the pump was off. Did you backflow the system before you turned it on to flush it. If there is an inch then I would really suggest getting it vacummed or a flocculant. I use an old broom to push it off the shelves and add extra filtration for a couple weeks. We used to breed tropical fish so I have a number of canister filters and stuff kicking around I use. I would also caution that a filter garden is great but to be really effective it would need to be about 3 x the size of your pond. Don't get me wrong you will see an improvement but it may not solve the problem. If you are so inclined you could try seeding the rapids with watercress it is an excelent choice for filtering through the roots. I redid my pond this year and have a huge bloom and I have never seen the plants look as healthy as they do right now even with very inclement weather conditions. I found an article years back about England using watercress in storm drains and sanitation ponds to clean the water. It seems to work and it does not mind swiftly moving water. Water iris is another one that I found lots of info as being really useful for that and they also do not mid moving water.
You might want to spend some time checking algae and water chemistry articles on some aquarium sites sometimes they come up with some interesting ideas and the more you know... What kind of clay did you use to pot the plants, is it reddish, that could be where the discoloration is coming from. Even rocks that look rusted, they will leach some color into water. Overall a healthy pond may have water discoloration without it being a problem unless it bothers the owner. Good luck

Sandy, the day you sound like a fourth grader.....forget it.... it "aint" gonna happen! Glad that some of my blather seems to be relevant. I sometimes wonder whether Im answering a question or just yacking into the wind.

Activated carbon. There are several factors in using and selecting activated carbon. Ive indicated a website/link below that discusses in general detail what activated carbon does without getting into too much theory. Activated carbon is made from all sorts of things: wood, coal, bone, coconut hulls, lignite (a form of coal-to-be), etc. The process is briefly described in the link listed below. To answer the question, yes, it has extremely large surface areas. The specification that is usually used is the "specific surface area", typically in units of square meters/gram of activated carbon. Values vary widely ranging from very low (100 sq. m./g) to very high (3000 sq. m./g) specially when looking at some of the activated carbon cloth. Another parameter you may see mentioned is the mesh size something like 8/12 or 10/24. This parameter refers to the granule size for granular activated carbon (such numbers arent usually used for powdered activated carbon) and, for example, means all the material passes through a number 8 sieve but not through a number 12 (usually referring to the Tyler sieve series). However the mesh size is NOT related in any significant way to the surface area! Think of activated carbon this way: look at a common household sponge - usually 3 inches x 5 inches by ½ inch thick or so. Notice all the pores. Now image a sponge that was at least 1000 times larger than your house but with the same pore sizes and pore geometry. Now you have an idea of where the surface area is located....not on the outside of the granule but inside. The pores of activated carbon vary from about 10 angstroms to about 50 angstroms depending on the quality of the carbon. But using the AC to get it to do what you want is an interesting problem. In an industrial or commercial setting 100% of the fluid (water or air/gas) will be passed through a bed of AC. Even then not all of the organics will be stripped out of solution. For an aquarium most designs have an AC held in place with filter cloth, "angel hair" or other physical restraint and the water flows through it (in some applications) or over it. But the pumps that most folks use in their ponds have a characteristic that makes it difficult to use AC by passing water through it: the pump curve or the rate at which the water being moved falls off rather rapidly with modest increases in back pressure (say a bed of AC). Furthermore, as the bed would also plug with solids (bactera, algae, sediment, etc.) it would bind or create even greater head loss very quickly. As a result most folks talk about putting a bag of AC in their system. At best this approach will mean that the AC will typically "see" about 1% or so of the water being processed at any one time. This is where our ponds differ from an aquarium. But as the water passes by the AC bacteria will attach and grow on it ... the AC offers an excellent growth medium. I do not know of any bacteria that will penetrate the pores (since the pores are so small) but the bacteria will colonize the outer surface with the result that they tend to cover up the pores. Think of it as putting a cork in a bottle! Some of the bacteria may come off with time but you probably will see a significant fall off in effectiveness of AC within a week or so but it also represents an increase in the bacterial surface area now doing its job just like your biofilter. So the net result that you still see an improvement but is it because of the AC or is it because youve now got an increased bacterial surface. I dont know....havent seen any studies out there that provide sufficient information to say. But I do know that our ponds and our pond water are not like that in an aquarium or the water coming out of a tap. Id like mine to be absolutely crystal clear such that a Sechi disk would give me a reading down to 400 feet! However, while it is clear and I can easily see each fish, pebble, etc. at the bottom I doubt if I could see much below 30 feet.

As to your question on carbon dioxide...I wouldnt try to regulate it or worry about it. Your pond is open to the atmosphere. You have some (hopefully minimal) algae producing carbon dioxide at night and consuming it during the day. You have fish, bacteria, etc. producing carbon dioxide 24/7. Given such an open system I highly doubt that you can regulate it nor do you need to as pointed out previously. If your growing things are above the water then carbon dioxide will not be limiting since they will take what they need out of the air...if I recall correctly!
David

David, maybe you can tell me if I am observing something correctly or just imagining it. Before I read the instruction to rinse off any AC dust from the AC before you put it in the water, I put all of it including the dust into a mesh planter. Of course as soon as the water flowed through, the dust washed off and into the pond. As soon as it hit the pond the water started clearing of tannins. I was quite happy with the results. The water did indeed look polished. Since I had not read that would happen I decided to continue reading and came across the rinse dust thing. OK, I thought maybe I had done something I should not and did it by the book. The results were finally successful after several days but didn't get quite the sparkle it did previously. I hammered some dry AC to get some dust, dropped it in and in less than an hour the water sparkled again. Now I don't rinse away the dust. What did I do, why did it work and should I stop? I often have a problem with tannins. The yard has several red oaks and sycamores and when the squirrels clean house a suspicious number of dried out and dirty nests end up in the pond. Sandy

Sandy, I'm here to report that the water jar test shows that I get fine green particles at the bottom of the jar and clear water -- though it is a small jar sample. I bet you're correct too in that this is dying algae or something like that.
I probably need a new filter media. I'm using last year's rinsed lava rock in two mesh backs beneath my bio-filter but as David has already said, those are often far too small.

Where do you find African Violet supplies (for the activated charcoal); specifically, what do you use and where?

David, Re: CO2. While most aquatic plants are taking it up by the plant leaves, might the lack of CO2 explain why my submerged oxygenators NEVER seem to take-off?

Sandy, if something works well then ignore anything anyone has to say about it!!! As to what is going on...my best guess is this: the dust from your activated carbon is nothing more than very fine activated carbon (obviously!). The dust is created by the granules breaking down in shipping and handling...they are rather fragile. However, making dust out of the granules doesnt really change the properties of the activated carbon. The actual particle size, as I mentioned above, or mesh size has very little impact on the surface area of the AC. AC is usually sold in granules but is also available as powdered activated carbon. Many water companies will add powdered AC to the water prior to running it though a rapid sand filter. So what youre doing is just making powdered AC with essentially the same properties (specific surface area, etc.) as the original granules. What is different is HOW it is coming in contact with the water. As I mentioned above AC in a bag only comes in contact with a very small portion of the water since not all the water is being forced through the bag. However, when you add the powder 100% of the AC is now available to do its job and does it before there is any significant bacterial growth on the carbon. With the bag method youll have bacterial coverage within a few days significantly reducing the capacity of the AC. As to whether or not you should keep doing it??? The old axiom "everything in moderation" comes to mind. I highly doubt theres a significant health effect on the fish or plants unless you dumping bucket loads into your pond but I am not a veterinarian and am very hesitant to make such recommendations. I know that people and pets can routinely take activated carbon tablets but thats not the same thing here. Again, if youre not seeing any adverse effects I guess Id continue to do it.

Pondbucket, if you have ANY alkalinity in your pond you will have carbon dioxide in your water. It might be temporarily above or below saturation but the equilibrium reactions between alkalinity, pH and carbon dioxide are very fast. At equilibrium you will have approximately 0.5 mg/L of carbon dioxide in solution at 25 C. The URL Ive listed below should allow you to pull up a graph showing the equilibrium relationship between alkalinity, pH and CO2. For example, if your alkalinity is 100 mg/L and a pH is 8.0 then the CO2 concentration is approximately 2.0 mg/L for a water temperature of 25C. This water is therefore supersaturated with CO2 and as a result CO2 will come out of solution as it is aerated. I have a spreadsheet that allows you to adjust for different temperatures but the bottom line is that for the conditions most of us run in our ponds (pH, alkalinity) we are almost always supersaturated with respect to CO2 to some degree. This, in part, explains why it is necessary to sometimes add sodium bicarbonate to your water periodically. I suspect it's the lack of other nutrients and/or grazing of your fish.
David

PB, I suspected the culprit might be organic debris from your description of the coating on the shelves that 'clumped' together. That quality is not normally seen in inorganic debris. The clumping is caused by bacteria growing in number and forming gelatinous colonies binding up the organic debris it is consuming. It is usually called mulm. At this point as the debris goes through your lava rock filters it is too small to be trapped. It has already been broken down repeatedly. You would need a much finer filter material to stop and hold it. Quilt batting would be an improvement but it will be getting dirty very fast and will require frequent rinsing or replacement. I suggest a shop vacuum with a pump feature to remove some of the debris quickly to get it down to a level your filtration system can handle.
David, please forgive my inability to process information as quickly as I should. After your last response I became uncomfortably aware you had essentially answered my questions about powdered AC in your previous posts. I have read this thread and links about three times now and I think it is getting through. At least I hope so. Sandy

Sandy...sorry to say this but you have made an error. You ASSUME that I remember posting those answers previously!!! LOL! Wait 'til you get old...life is great meeting so many new friends each day (the same ones from yesterday!).
---David

I wanted to post a follow-up to this great discussion; it has been a great help to me. Thanks Squirelette, David (drh1), and Sandy.

I started cleaning my system at the tail end of the pond by the skimmer; I removed and cleaned the leaf basket, no biggie. I temporarily removed the pumps in the skimmer basin, I have two pumps there, and cleaned the intakes with a strong stream of water. I then cleaned the vertical poly mat filter (I was doing this nearly every week already, but I had fallen behind).

I then restarted both pumps.

Moving to the head of the pond... (I must say, I was under the false impression that you shouldn't really ever clean the filter components at the bio-falls.)

I started by cleaning my poly. filter mat at the bottom of my bio-falls basin. Man was that thing dirty. I then removed one of my two mesh bags of lava rocks. I left the one bag of lava rock in the middle of the bio-basin since I thought it would contain startup beneficial bacteria. In place of the mesh bag of lava rock that I removed I supstituted it with the Savio Springflo filter media, only about 3/4 of the whole spool would fit, and then I covered that with my plants in mesh pots.

I added Accu-Clear, a flocculent, single dosage to to the perimeter of the pond. And for good measure I added 'round 16oz of activated carbon pellets (couldn't find the larger pieced type) to a small mesh bag and placed it in the skimmer basket.

It has been about three days and the water seems to be clearing nicely.

Now I wonder if I should actually stir-up the MULM sediment on the shelves or bottom of my pond to get that stuff to the filter media.... then clean the filter media once again?

Pondbucket, if I may suggest that you do not stir up the mulm on you pond's shelves and bottom.
There are pathogens living in that mulm that could possibly create a parasite infection to your fish.
Your fish would have to swim in the dirt laden water, taking in whatever it contained, after which they filter the water out through their gills. Not a good idea.

As Sandy suggested, vacuuming the mulm up would be better way of cleaning it up.
You would not stir it up as much dirt as you suck the debris out from your pond bottom.
Cleaning the bottom/shelves off, is always going to disturb the junk and cause the water to cloud, but it is best to try and limit the amount of clouding.
"Horton"

If you wanted you could try a "Python" from the local fish store to clean up some of the mulm. It is made for cleaning aquariums, I have one and use it occasionally when the fish dump over a plant. It is not the greatest tool because it wastes a lot of water, you hook it up to a tap to create the suction needed. I tie it on to the end of a pole and use it to suck up the mess. They run about $50.00 for the 25' hose. Not the greatest but cheaper than a pond vac if you have the patience and don't mind running the tap for a while.

Good info on this thread. When I started my pond up this spring I had left the bag of filter media in the pond then transferred to biofalls. Last weekend I shut off that falls, swished the media around alot and dropped it back into the pond while I drained the barrel--couldn't believe the crud that was in there after 3 wks of pond running. I use koiclay on my pond regularly and it really seems to help with algae blooms, water clarity and plant growth. If you look up vegefilter or plantfilter for ponds on the net you will find that they do require a large filter per pond area and recommend yearly removal of plants and cleaning--so if that's what you want go for it. I've tried hyacinth in my waterfalls containers but find it backs up the falls. Wish my shopvac was bigger as only 6.5 gals--in about 30 seconds is full! Thanks for info on stirring up bottom mulm Horton--never thought of that danger.