I've found that digging around a river or stream to change its shape greatly decreases my frame rate. Would pumping out some water have the same effect, if I stop the pump afterwards?
If the water you pump out does not move around a lot, it should have no appreciable effect on FPS after the riverbed fills back up to capacity.
To maximize FPS, try to make sure there are no partial water tiles (below 7/7), though that could be difficult if you're going to be using the water. Minimizing the surface area of the reservoir could lead to lesser number of partial tiles moving around, though the benefit is likely to be minimal in common scenarios (Surface area of 100 tiles or less).