This is a matter of water current speed and the size of the fish you want to sample. Normally, fish can withstand current speeds up to about four body lengths per second (sustained swimming speed).So, if the current speed is higher than about 4BL/sec the fish would be pushed down by the current.
There can be much difference in water velocity in the vertical cross section of the running water body. One could expect a reduction of the current speed due to friction towards the bottom and the sides. In this context, if the current velocity is lower than about 4BL/sec you are likely to find aggregation of fish at the head waters, subject indeed to various other biotic and abiotic factors.