The River brown trout (Salmo trutta fario) is one of the freshwater fish species that is endangered in Iran due to overfishing, habitat destruction and demolation of special substates for spawning. Three sampling sites were considered from different parts of Chalous River (upstream, middle and downstream of river) to predict the habitat suitability of the River brown trout. A set of environmental variables (physico-chemical and structural variables) was monthly sampled at each sampling site (in total 19 variables). The environmental variables were simultaneously colledted with the presence/absence of the river trout (12 samples presence and 24 samples absence) during one-year study period (2017-2018). Based on the prediction of the generalized linear model, there was a significant difference between the presence and absence of fish in the sampling sites regarding all the environmental factors (after excluding the variables with high correlation) (p< 0.01). The results of the model showed that increase of the water flow velocity, river depth and dissolved oxygen concentration (especially in the upper part of the river) may increase the probability of fish presence in the river. In contrast, increasing physical and structural variables such as water temperature, the river width and the distance from the source and also increasing the concentration of water quality variables such as salinity, nutrients (such as nitrate and phosphate), chemical oxygen demand and suspended solids gradually might decrease the presence of fish.