My direct experience to your specific question Is limited. Years ago, I helped fish biologists sample a section of moderate velocity water, resulting in some likely mortality. As hydrologist, I measured the flow rate and they installed nets above and below the sample section. They had equation on how much rotenone to add at upstream net, and how much potassium permangenate to deactivate the rotenone at the downstream net. The stunned and possibly dead fish and probably aquatic insects floated down into the lower net, perhaps about 100 meters downstream for a sampled stream about 10 meters wide. All organisms caught were identified, measured, weighed, pictures taken, samples preserved as desired, etc. as appropriate.

All the more recent testing and sampling that I was infrequently involved with or aware of over the last several decades used fish shockers, hand nets, etc. Professional fish and aquatic biologists conducted this sampling, sometimes volunteers were included. As a rule of thumb, if velocity of river in ft/sec times depth in feet is greater than 10, wading should not be attempted for measurement, and especially for shocking. If substrate is slippery, wading and shocking can be hazardous. The person doing shocking must be ready to shut down if those netting slip in water over waders. With a boat, more powerful generators can be used for shocking if you can figure ways to sample and collect fish by boat with netting. Shocking and sampling, measuring, weighing, identifying may or may not cause mortality. Most rivers contain various habitat units, but in fast flowing rivers, these may be difficult to evaluate and gain effective, representative samples. I have known some fish biologists use scuba gear in slow to moderate flowing streams and rivers to visually check diversity or take underwater movies. As velocity increases, the safety risk also increases for diving, underwater hydraulic suction through cracks in rocks, etc. With technology today, perhaps someone has developed water proof videography capability, powered by an underwater drone or submarine with remote control and real time video link. As velocity and turbulence increases, at some point the combination of air bubbles would eventually be too much. Turbidity and sediment are added issues. Very fast waters may have difficult to safely sample habitat units in coarse substrates, large wood debris, boulders or bedrock.