Pond rocks turning black and winterizing a pond

Question
Hello - I live in Maryland and have a small (500 - 750 gallon) pond with 2 pumps and about 4 pond plants.  It is a haven for birds, toads and frogs and we truly enjoy it.  Last year, the pond was infested with a hairy algae that did not go away with the winter freeze, so this spring, I pulled out all the rocks and plants, gave the entire pond, including the rocks a good cleaning/scrubbing and re-established the pond.  I also purchased pond pads to keep down the hairy mess.  Good news is that now, after the pond has balanced,the water has remained nice and clear, but all of the stones and rocks in the pond are turning black.  Is this an algae of some type?  Is it harmful to the pond?  Is there anything that I should do to keep it under control?  

Also, is there anything special I should do to winterize the pond?  I've had it for 2 years; I leave the plants in the pond with the pumps running and place a small heater to keep ice from completely freezing over the pond surface.  Is there anything you would recommend that I do in the fall or spring to ensure that the pond stays healthy?  It is quite a challenge to keep out leaves, pine needles, etc.   

Your response to the 'black' rock syndrome I'm experiencing and any suggestions for winterizing are very much appreciated.

Answer
Hello Tina! The good news is that the black color of the rocks will not hurt the pond or wildlife. It's completely normal and it means that your pond is indeed "growing". This explains your clear water. The black is algae, sludge, patina, and other organic material feeding on fish waste and other compounds that form in the pond. Periodically, every few years or so if the pond is maintained properly, you will have to do what you already did...clean everything out and scrub it down.

In addition to your current winterization practices, I would recommend a pond cover net. They are available in a wide array of sizes and are inexpensive. Pond cover nets will keep you from having to go out in the winter and get the leaves/debris out on a regular basis. A small air pump may help with any algae problems and keep the growth on your rocks to a minimum. In the winter time there always seems to be an increase in the amount of organic debris breaking down in the pond. This breakdown takes oxygen out of the water and that takes away from other vital functions. If you are using beneficial bacteria throughout the season it's a good idea to get a winter blend and use it through the winter. Spring clean outs and openings seem to be easier with cool weather bacteria use.

Hope this helps Tina!