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We examined changes in physical habitat structure, temperature condition and their possible effects on the structure of Danubian fish assemblages due to the outflow of the Paks NPP's warmwater channel, in Hungary. Seasonal surveys conducted both upstream and downstream from the outfall showed that its hydromorphological effects were generally local and comparable to natural or other anthropogenic hydromorphological changes. The effect of the returned cooling water was more apparent in the seasonally recorded surface water temperatures and depended highly on the spatial positioning of the sampling sites. However, environmental and spatial variables accounted only for a low amount of variance in case of both shoreline and offshore fish assemblage data. Overall, we found that the outflow exerted only a local scale effect on the structure of Danubian fish assemblages. 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