Understanding spatial distribution of organisms in heterogeneous environment remains one of the chief issues in ecology. Spatial organization of freshwater fish was investigated predominantly on large-scale, neglecting important local conditions and ecological processes. However, small-scale processes are of an essential importance for individual habitat preferences and hence structuring trophic cascades and species coexistence. In this work, we analysed the real-time spatial distribution of pelagic freshwater fish in the Římov Reservoir (Czechia) observed by hydroacoustics in relation to important environmental predictors during 48 hours at 3-h interval. Effect of diurnal cycle was revealed of highest significance in all spatial models with inverse trends between fish distribution and predictors in day and night in general. Our findings highlighted daytime pelagic fish distribution as highly aggregated, with general fish preferences for central, deep and highly illuminated areas, whereas nighttime distribution was more disperse and fish preferred nearshore steep sloped areas with higher depth. This turnover suggests prominent movements of significant part of fish assemblage between pelagic and nearshore areas on a diel basis. In conclusion, hydroacoustics, GIS and spatial modelling proved as valuable tool for predicting local fish distribution and elucidate its drivers, which has far reaching implications for understanding freshwater ecosystem functioning.