No, you need to run the aeration system continuously. What harm are you talking about? The aeration system will continuously circulate the water from top to bottom, it will bring oxygen rich water to the lower region of your pond where it will support the break down of the organic material that has been accumulating for years. The zooplankton will be able to exist through out your water column and feed upon the planktonic algae, the small fish will eat the zooplankton, allowing your pond to support a healthier population of fish. Are you experiencing run off of fertilizers? What is your surrounding watershed?
