Cleaning your submersible pump and motor should be done regularly while in use, at least once every three months. Remove the system from the pond and tilt it at an angle making sure all water has drained out. You will need to then scrub any green algae covering the pump and motor. Using a stiff brush and hot soapy water should take care of this. Make sure you clean your system thoroughly as any mud or algae buildup may clog or prevent your system from working properly.
After cleaning the system you will need to check the filter. Depending on the manufacturer filters are either disposable or may be cleaned and reused. If they are reusable, you may use the same stiff brush and soapy water; make sure that any debris is removed from the filter's surface. The filter must be completely dried before it is reinstalled.
If you live in a part of the country with four seasons, and in particular northern areas with harsh winters, it is advisable that you remove your pump and motor completely until the spring. If left underground during the winter, water in the pump and motor will freeze and can crack the lines leading to the pump as well as damage it and the motor itself. This almost always results in the need for a new pump and motor, which can be very expensive.