This thread may be old, but the subject will continue to be relevant as long as people own ponds and water features. That subject being---ALGAE. It has been around for millions of years and, regardless of man's ingenuity, it ain't going away. Did you have the algae before you went on your boat trip? Brown algae is extremely rare in freshwater. I would suspect that either the algae is dying or it is just coated with sediment/silt giving it a dirty appearance. Algae, because it is living organisms, in particular... mini-plants, will not proliferate unless it has a good supply of nutrition. The higher the chronic nutrient levels are in a particular body of water, the higher will be the incidence of algae proliferation. A certain level of algae is both acceptable and desired. Control the nutrient levels and you will control algae growth. Sufficient aquatic plantings should keep the NitrAte levels too low to promote most algae growth. Attention should also be given to the level of Phosphorus which is also a plant nutrient and commonly overlooked. Any P level greater than 5 ppm will encourage rampant growth of some specie of algae, most particularly 'String Algae, which absolutely thrives in warm moving water high in Phosphorus. I am not going to address in depth the use of ionizers or ultrasonic devices nor the use of chemical or enzyme based products for direct algae control as NO studies have been conducted on the long term physiological effects these products may have on fish or other aquatic life. Others may disagree, but most of these products are 'Snake Oil' at worse or misrepresented with half-truths at best. Yes, you should clean the filter pads, not the filter media, in both the skimmer and the biofalls unit as often as needed. They are performing the function that is intended...filtering.