If you dredge, also have the stream re-directed around it if possible.

Try to snag runoff from other sources or rely on water flowing through a good batch of soil as a filter.

There is a beautiful pond near me with a small stream nearby that a person would think as an ideal water source to keep it topped off, but instead they re-directed the stream around it. Fortunately there is plenty of ground water, being in the same basin, to keep it topped off. This pond is the envy of the area, except right near the road.

10 years old now, and pristine as the day it was dug. I have seen the stream flooded many times with no ill-effect on the pond.