The influence of a nuclear power plant's cooling water and physical structure on benthic cover and fish communities were assessed in a coastal area in Southeastern Brazil. We hypothesised that thermal discharges decrease benthic cover and consequently, change the associated rocky reef fish assemblage structure and that physical structure is directly associated with fish richness and diversity. Twelve sites at different distances (close, near and far) from thermal discharge and types of physical structure (low and high) were sampled by visual census. The average surface temperature at the most impacted sites (close) ranged from 30.5 to 31°C, while at far sites it ranged from 25.5 to 28.5°C. Although thermal influences have decreased benthic cover, and consequently, decreased fish richness and diversity, we found that in near and far sites that had complex habitat structures (physical and benthic cover) fish communities were unaffected. The greatest abundances of Eucinostomus argenteus, Mugil curema and Sphoeroides greeleyi were associated with the highest temperatures at the most impacted sites. In contrast, Abudefduf saxatilis, Chaetodon striatus, Stegastes fuscus, Diplodus argenteus and Malacoctenus delalandii were more abundant at high structured sites far from thermal discharges. Our data support the hypothesis that thermal discharge decreases benthic cover, fish richness and diversity but physical structure, when coupled with high diversity and abundant benthic cover, minimised thermal effects on fish communities.