The real impact on downstream fish populations of a change in management of a hydropower installation, in particular, the impact of an increase in instream minimum flow, can be difficult to assess. Other factors, in addition to the simple habitat limitations in low-flow periods, can influence the evolution of a fish population over time. It has often observed in French streams that the 0+ individuals appear limited by strong discharge in the first months after their emergence (March to May). A dynamic model of a trout populations (MODYPOP) has been applied to the river Roizonne in the French Alps, upstream and downstream of a hydropower station, in order to estimate the effect of different discharge time series on trout population dynamics. Trout populations were monitored by means of annual inventories at two study sites, one with minimum flow and the other with natural flow. At each site, available habitat was described and simulated as it changed with discharge, according to the ‘microhabitat’ method (EVHA, derived from PHABSIM). Habitat time series were built on the basis of discharge time series. MODYPOP simulations, integrating habitat and discharge time series, were compared with observed fish numbers. Results indicated that fluctuations in discharge during the post-emergence period played a major role in the dynamics of the total population. Predictions were significantly improved when the impact of strong discharge on emerging fry was integrated in the model. Copyright © 2003 John Wiley & Sons, Ltd.