In recent decades, brown trout populations have been declining due to river regulation and its impact on river morphology along Lar River downstream of Lar Dam located near Tehran. Currently, due to water scarcity in the country, intensity of water regulation impacts on aquatic population of streams and specific ecologic values in tributaries of Lar River, it is necessary to present a habitat assessment model to predict ecologic response of the river to natural and man-induced changes by which can be applied to strategic management of the river. Hence, in this research,an analytically applied approach is adopted to assess brown trout population by creating relation among hydrologic, hydraulic, morphologic and ecologic processes. After field work and required measurements, Shields function was applied to derive dimensionless shear stress for minimum environmental flow, bankfull discharge and critical discharge for initiation of sediment transport for Lar, Dalichai and Sefid-Ab rivers. Then, dimensionless shear stress for initiation of the bed sediments was used to investigate effects of discharge variation on frequency and distribution of aquatic life in response to morphologic changes. It was found that when water discharge is in the range of discharge corresponding to environmental flow threshold and critical discharge for sediment motion, it is identified functional discharge for bed occupation while water discharge greater than critical discharge for sediment motion is also considered functional discharge for bed preparation. Results obtained from this research, suggest that water discharge, cross-sectional geometry and bed material size could be effective on ecologic functions and life cycle of brown trout fish and inappropriate river regulation may lead to gradual elimination of that from river ecosystem.