Sure looks like one of the fungal diseases. A lot of brown patch in the northeast this year due to all the rain and humidity. Not sure what it has been like where you live, but if it has been wet and humid where you live then it is highly likely. You can tell it is a fungus by how it looked throughout the disease cycle. I doubt it's cat pee, because cats generally dig a whole in the dirt and then pee in it, but anything is possible.

Adult koi need about 1000 gallons per fish, but if you are very regimented with your cleaning tasks and have a really decent sized filter, you can get away with less. First of all, you need to get all of this "sludge," out of the pond, and you have to do it often. Also, change the water. Not all of it, but a portion. The more you do it, the less you have to do at a time. Secondly, your filter. The easiest way to cheat on the "gallons per fish," rule, is to oversize your filter. A large filter will increase the volume of your pond, and a bigger pump will turn over water faster. The more water you have, the bigger the bioload the pond can sustain. The small filters sold in places like Petsmart aren't really the way to go in this situation. You're better off making your own or buying from a pond supply store. Third, algae. Algae is pretty much the most persistent form of life on the planet, if you ask me, and throughout the life of your pond, you will battle with it. .Algae feeds on the nutrients in your water. The more nutrients, the more algae. Your nutrients are coming in the form of fish food and waste. Koi are big, dirty fish, and they put a lot of "nutrients," into the water. A UV filter is not going to do anything for a pond that's way overstocked. Algae is not ALL bad, however. Having small amounts of it will help keep nutrient levels down. In a healthy system, your aquatic plants will absorb most nutrients, keeping the water clear, and out competing algae. Algae will always be around in some form, however, and that's okay. It's the huge blooms of it that you're trying to avoid. Fourth, the fish. Personally, I love koi - they are beautiful, endearing fish, and they are a joy to keep. But they are demanding. They need lots of room to grow, and a small system just isn't the place. You're better off with comets, which stay much smaller than koi, but also come in a good range of colors. If I were you I would try to give some of the fish new homes. Basically, what's going to keep your pond clear is hard work. On a seperate note, the whole bioball system is rather questionable, and many people find that over a period of time they begin to contribute large amounts of nitrate. They are designed to excel at breaking down ammonia, but overtime waste gets trapped in them and thats where the problem comes from. You might want to research that. I wish you the best of luck. =)

The fungus spends the winter in infected plant debris in or on the soil where it can survive at least one and perhaps several years. It can also be seed borne. New spores are produced the following season. The spores are transported by water, wind, insects, other animals including man, and machinery. Once the initial infections have occurred, they become the most important source of new spore production and are responsible for rapid disease spread. A thick mulch indeed does help against splashback and also serves to keep moisture in. A good organic mulch will also decompose and compost in place. Compost makes for healthier plants which are better at fighting off diseases. In fall I clean-up as best I can by removing all plant material. I use a straw mulch and remove that as well and place into the compost pile. I then lasagna compost with a mix of grass clippings, shredded leaves and new compost on top. I plant right through that in spring and then straw mulch again.

Before doing any more, or allowing people that do not know what they are doing spray something else, tak samples of this shrub and place them in a sealable plastic bag and take it to your local office of the University of Florida Cooperative Extension Service. They will identify what the problem is and what the appropriate means of control might be. http://sfyl.ifas.ufl.edu/map/index.shtml