The paper reports the development of an individual-based fish dynamics model, of which the key components are the rules for the movement of individual fish and the definition of the habitat suitability. The distribution of the fish mainly depends on the flow conditions (velocity, depth, substrate) and life cycle of the fish. A major contribution is the refinement of the rules for fish movement, based on laboratory experiments under volitional swimming conditions, which also provided the ranges of preferential velocities and substrate size for the target fish, Spinibarbus hollandi. Moreover, they provided data on the fish trajectories and distribution patterns that allowed for validation of the movement rules. The validated fish dynamics model was applied to investigate the effect of discharge increase during the dry season by means of reservoir operation in the Lijiang River, which was the subject of field investigations in 2007 and 2008. The model results indicated that reservoir operation leads to an increase of fish biomass. According to the fish movement rules, fish cannot always escape from riverbed regions that dry during decreasing discharge events, which causes them to be trapped and die. Reservoir operation decreases the area of dry riverbed and reduces the travel distance for fish to escape from dry regions. Critical advantages of the individual fish model over global models defined on the population level are that they can account for the time that the fish needs to reach a region of suitable habitat and for the spatial pattern of suitable zones and their connectivity. Copyright © 2013 John Wiley & Sons, Ltd.