Don't repot your lilies now. They are going to be lovely as all those blooms open up. If you repot them now you will lose all those lovely flowers for this year. This picture doesn't really show how big or deep the pond is so I am not sure they are overgrown but the fact they are growing so well after that much neglect is proof something is going right. There is obviously a pump that is working. What kind of filter is there? What kind of liner? How far up does it go behind that great rock? Did the fishies come with the pond?
I would work on clearing up the water and pulling out the muck on the bottom but it should not be necessary to completely empty the pond. Get rid of the dead foliage. If you make too much work out of it, it won't be the pleasure it can be. We are pretty patient here with newbies and we want you to succeed. We have been where you are now although I have to say you are lucky you didn't have to dig it out and haul all that stone. Sandy

Wow, that's a lot of lilies! Yay for you!!! And what a gorgeous pond you have. I don't have any advice, I still consider myself a newbie at this too. Just wanted to comment on your lovely pond!

Sandy-
I took another picture so that you could see the whole pond. You can see a spot that we already took out the lilies. I guess I thought that the lilies weren't supposed to cover the entire pond- is it ok if they do? I'm not sure what kind of filter it has. The liner is a black material. The fish did come with the pond. We didn't even see them for awhile after we moved in. The guy that sold us the house told us that the pump didn't work but after we cleaned it out it started working just fine. The deepest part of the pond is right under the waterfall. But the rest really isn't that deep. So how would you get all the muck out. The problem we were having last week when we were trying to pull it out was that it was all mixed up in the roots of the lilies and we couldn't get it out without taking out the lilies. Sorry this post is so long! I think that we are lucky that we didn't have to put the pond in!
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Most of us would be thrilled with the proliferation of your lilies. They are lovely and perform a normal and important element of the pond ecology. They shade the water and prevent the growth of algae. They also provide shelter for the fish and any future progeny. Water lilies do best in calm water so if you remove some it is best to pull them away from the waterfall.
It is true that having the deepest part of the pond under the waterfall is not the best idea but it is not a fatal error. I have the same setup and when I vacuum the bottom the muck and debris cloud up a little but not enough to be a problem. The secret is to move the nozzle of the vac very slowly and check for clogs often. Whole leaves and twigs are the most annoying. If you think it is a problem, you can always turn off the waterfall while you clean. It is a shame the former owner did not show you how it functions. No two setups are the same and it can be confusing to an experienced ponder as well as a newbie. Since you have had the pump out without any such problems the following caution about turning off the pump is not relevant.
When you turn off the waterfall it is important to know how the filter functions and where it is located. In some systems, turning off the pump without closing the tubing from the pump to the filter can cause a back wash which will drain the water from the tank back into the pond. This is not good. Find the intake hose that is somewhere in the pond and see where it goes. Eventually it may go to a tank behind the waterfall and that would be where the main filter is located. This kind of filter only needs occasional cleaning. There may also be a pre-filter installed in front of the pump that prevents large debris from entering the pump.
If the tubing goes only to the waterfall look for a kind of box located in front of the pump. That would be a different kind of pre-filter and it will need cleaning ever so often. As there are many kinds of filter systems you should try to figure it out sooner rather than later.
The grasses definitely need a haircut. As large as they are, they will block new grass growth except on the outer edges. In the grass garden, they use either an electric hedge trimmer or chainsaw. Dead grass foliage dropping into the pond can easily clog up the impeller in your pump.
Please let us know the where and what of the tubing, pump and filtration system. That way we can give you more precise information. It isn't a good thing to confuse you with a lot of info that really isn't relevant to your pond. If you want to learn about other types of pump/filter systems you can do that later. It's more important that you know what you have now.
Thanks for the photos, Sandy

You've got yourself a nice little pond. I like the way the plants are growing around the waterfall. If you feel the lilies are a bit too thick, you might want to just thin out the excess lily pads down to the bottom of the stem. I did that last year when they took over my pond. I repot in early spring, before they start perking up. I must say, your lilies look very happy and seem to be getting everything they need to be healthy.

Like Sandy said, you might also want to pull them back from the waterfall a bit.

Thank you guys so much for the advice and suggestions! I really appreciate them! Sandy - when you say vaccum out your pond do you mean with like a Shop- vac? And when you do that do you drain out some of the water first? Also do the fish just stay away from it? (I'm guessing they would because they become skiddish when I walk around the pond trying to look at them.) For the pump and such, The pump is hidden between those two grasses (on the left side of the photo) and then a hose goes all the way around the outer edge of the pond and up to the top of the waterfall where there is a big black circular bucket looking thing that the water spills over (I'm guess the black circle thing is the filter? Also in the pump is a kind of like foam filter that we took out and cleaned not too long ago. I hope all of that info helps sorry I'm not too technical! :-) So I am guessing that with what you guys said that we should just leave the lilies alone for this year try and move them away from the waterfall as much as possible and just thin them out. Also just try and clean out the muck as much as possible off of the bottom of the pond. Thank you so much for all the info!
Sarah

Some of the muck in the bottom can be scooped out with a pond net (WMart, Lowe's, etc). And yes Sandy means a Wet/Dry Shop Vac, no need to drain any water before. Use the dirty water on the other plants in your garden.
Whenever you stir up the water in a 'dirty' pond you need to check that foam filter on the pump frequently for a few days after - that suspended muck will clog it up pretty quickly.

One other thing. If you have city water, or have chlorine in your water, you must add a de-chlorinator when you add water to your pond. For instance, if you vacuum out 20% of the water along with the muck, add de-chlor when you fill the pond back up.

I don't know any exact amounts 'cause I use well water (non-chlorinated) so I've never used it, but it's important for the health of your fish. Small water additions aren't usually a big deal. (Somebody else here help her out please, just follow the directions on the bottle I assume?)

I would wait 'til early next spring to re-pot those lilies too. Search this sight for 'how to'. They've been crowded this long, what's another year?

What fun! Congrats on your new home and pond!

One thing you will need to purchase and learn to use is a pond test kit. Doing a test every week or so allows you to keep your water healthy and clear. Things that can mess up water chemistry are overfeeding, fish poop and other organics like the muck at the bottom of the pond, heat, insufficient oxygen, rainwater and a bunch of other things. Most of the bad things can be caught early with the test kit. Don't waste money on test strips. They are often inaccurate.
Not all shop vacs are designed to pump out the water continuously. It will say on the box that it has a pump feature. I found mine for $85. There are other devices that work with water running from a water hose. The one I use most often for a quick fix is this type. It's found at WalMart and is for childrens pools. It costs $20. I am looking for one of a similar design with better construction. It is just plain flimsy and repairs don't last. Python also puts out a similar device. It is hard to hold, the capture jar is too large around for me to open and it is overpriced at $89.It is complicated.
The shop vac removes water. You can run the hose that you attach to it to your garden. The dirty water is good fertilizer. The other two add water to the pond so I pump some water out with a sump pump or I drain the filtration tank. Either way is simple to do, even for someone with my current physical problems. LOL, sometimes I must be a sight to see. The fishies sometimes get curious but if you keep the nozzle moving slowly, they will lose interest without getting scared.
Are you saying the pump and tubing are not submerged? If so, it is a different type of pump than I use. That isn't a problem but we need to get another forum member to discuss them. Mine are submerged and I hesitate to give advice on a type I have no real experience with. The other things function enough alike that I don't have a problem talking about them. If I do, someone else will be along.
While the pond is dirty, that foam filter in front of the pump will need to be cleaned fairly often, just like Sheepco says. Most pumps can handle dirty water with some small abount of debris but larger debris needs to be stopped from going into the impeller as it can cause damage. I hate that tiny little filter. It is just too inefficient for words. I found a prefilter for a well pump at Menards. I used some stepdown PVC connectors, also at Menards to make it fit the tubing. It keeps anything above the size of a small pea from entering the pump and a decent pump can handle that with no problem. I threw away the tiny foam filter that came with the pump. The water exits the pump and tubing runs to a 100 gallon Stock tank which is my mechanical filtration It also serves as a home for the bacteria that cleans up organic matter in the water. That black bucket thing behind your waterfall is likely to be a mechanical and bio filter. The details are just a little different. My filter is called a Skippy Filter. It is not the only design out there. I just happen to like playing with this kind of stuff. Another small pond I have the care of changes drastically every year. No matter what kind of system you are using you should look at how effecient it is, whether it works for you and if it does what it is supposed to. There are many sites that explain how filter systems work. To see how my skippy works, google Skippy stuff. My pond is 1000 gallons so my system is probably oversized, but I want to enlarge it this year or next. I have to get my body working first then I can use it as physical therapy!
You have either EPDM or plastic(PVC)as a liner. If it feels like rubber it is EPDM. EPDM is rubber, just like they use in innertubes or on roofs. 45 mil is best but it comes in a thinner version as well. The plastic liner isn't as durable but some people do like it.
To figure out how many gallons your pond holds(useful for medications, additives, pump size, etc.)go to the link named pond volume calculator at the end of this post. Then you can figure out how much water you have, how much your pump should be moving, how many fish inches you can support and all sorts of other things. If you don't like this one, there are others. That is likely to be enough for now. As you think of questions just add on. Enjoy, Sandy

Here is a link that might be useful: pond volume calculator

Check to see if you have a pond or water gardening society or club in your area. That's one of the best ways to learn how to care for you pond and fish. I joined one here in Tulsa, and they've been a wealth of information. They only meet once a month, so it really isn't hard to find the time. If your city has a pond tour, that's another way to meet other ponders and learn about them. Ponders love to talk about their ponds and are more than happy to help out any way they can.

It can seem a bit overwhelming at first, but ponds are really pretty easy to take care of.