Bottom-dwelling fishes with low swimming capacity burrow into soft substrates or occupy shelters, such as stones and vegetation, to reduce metabolic costs of holding their position in running waters. As a consequence, under natural conditions it can be difficult to examine the effect of water flow as the limiting factor of benthic fishes. The velocity (0, 10, 20, and 30 cm s−1) preferences of spined loach and Northern golden loach were examined experimentally in an isosceles, cross-shaped acrylic tank with five square chambers (side of 15 cm and 40 cm high). Fish could select freely between a sheltered place without water flow (two side cells) and with flow (three) cells. Fishes were observed for 40 min by taking time-lapse photos every 0.5 min, with the first 7.5 min (= 15 photos) treated as an acclimatization period. Each treatment was repeated 10 times with 65 photos analysed. The disparity between the proportion of fish observed in the active and passive areas of the tank was used as the preference or avoidance of the velocity treatment. Northern golden loach showed a random distribution between cells (no bias from a proportion of 3:2), only at a velocity 0 cm s−1 revealing strong preference for water flow 10 and 20 cm s−1 and avoidance of velocity of 30 cm s−1. Spined loach preferred a velocity of 10 cm s−1 and avoided velocities of 20 and 30 cm s−1. Surprisingly fish were not randomly distributed at a velocity of 0 cm s−1, at which they were more frequently found in passive cells than active ones. The results confirm that Northern golden loach is a rheophilic fish occurring only in running waters, whereas spined loach is an ubiquitous species distributed in slow-flowing as well as stagnant waters.