Pond cleaning questions

Question from a pond keeper:

I have had my pond for three years now. the bottom is covered with small rocks about 3 inches deep for natural bacteria surface. The water has been crystal clear for the last 2 years. Its 6 ft x 12 ft, 3 ft deep. I use a skimmer and biofalls system, with a 4000 gal/hr pump for 1000 gal water. I hear you say to clean out the entire pond every year. Others say to let it ride.

Some of my plants have even escaped the plastic pots and have rooted into the rock bottom. I change the water regularly. Is there any harm in letting it go without eliminating the bacteria colonies that have built up in the bottom? I'm thinking .... if its clear, and not broken, don't fix it? What do you all think?

Pond Expert Carolyn Weise answers:

You have more than a substrate of rocks down there by now. You have a layer of silt that is building up into a living layer of soil, which is anaerobic. If you decided to empty the pond and muck it out, you would know in an instant how awful it was. With ponds, it really isn't out of sight out of mind. What you do not see can really be a problem waiting to happen.

Reply to Carolyn's answer:

What sort of problems could this cause? in the summertime, I have to change my filter daily, the koi waste plugs it quickly. and when I rinse it out, if I let that water sit for a day or two, it does smell like sewerage. (but all my plants and vegetables love it, makes them grow good), really the only thing i check for regularly is the ph levels. If the fish do not eat when I throw in food, I know somethings up. or after a long rain, that always brings it down. I just add baking soda and its back up. What else should I be looking for?

Carolyn replies:

You just mentioned a few very important ones. The idea that the fish would not eat is a very serious one and should be prevented at all cost. It is significant of poor water quality. Remember, all water toxicity is not visible by the naked eye and pH is not the only parameter that affects your fish health. The pond is a big part of your biological filtration. If not kept clean, the water suffers greatly, ergo, do the fish.