It really depends on a lot of factors, including water quality, substrate composition, and the extent of the digging. The majority of microbial activity in most waterways isn't in the water, but instead in a region called the hyporheic zone, a surprisingly thin layer of sediment at the interface between surface and ground water.

Digging and dredging both are fantastic ways to disrupt this layer. Microbial communities will redevelop rapidly, but their composition will be different. The makeup of the stream/riverbed will have significantly changed; different types of microbes reproduce at different rates, with fast reproducers initially crowding out slower growers; and the products of the activity of some microbes provide the conditions under which other types of microbes can flourish. The composition will change over time and may take months or even years to return to a steady state, and even then that state may be quite different than before digging or dredging.