if weather and sun are the factors to change your ponds water quality i am guessing it's algea?
i am not a pond expert but only recently installed several small ponds at home. as starting plants i grow water hyacinth, pistia and azolla as pond cover, hornwort, watersprite and eichhornia diversifolia submerged, and i try to go by the rule of thumb of having maxium half of the water surface covered. in fact, if there is more than half of the surface covered the water will be very clear and the fish and tadpoles appear a lot more hungry, so i am thinking the hyacinth and pistia with their long submerged
roots are cleaning the water too much, and i try to throw some of them out as mulch or
compost before this happens. so, i agree with what Devon said, the floating plants do a lot of cleaning in the pond! and they are fast growing and easily removed.