Habitat conditions at multiple scales are one of the major factors structuring ichthyofauna. Thus, we analyzed the fish habitat associations along the headwater-mouth gradient of a coastal Atlantic stream. We categorized the sampling sites into habitat units, so that in the middle reach these categories were statistically differentiated into riffles, runs and pools. Samplings were carried out quarterly from May 2009 to February 2010 using electrofishing. Principal component analysis (PCA) indicated an environmental gradient from higher water velocity and rocky bottom to deeper and sandy areas in the headwater-mouth direction. A total of 1,495 individuals belonging to 27 species were captured, being 13, 18 and 22 from headwater, middle and mouth reaches, respectively. Shannon diversity was slightly higher in the middle reach, while beta diversity showed higher rates of addition than turnover in species along the longitudinal gradient. Fish structure, evaluated by DCA (detrended correspondence analysis) scores, showed significant differences between upper reaches and mouth reach, but the middle riffles did not differ from headwater habitats. In the middle reach, mesohabitat analysis distinguished riffles, with higher abundance of fast-water crenuchids, from pools, with a higher abundance of lentic-water characids. These results suggest that environmental differences along the stream determine the wider structural patterns. However, the middle reach amassed species from upper areas and lowlands in structured fish mesohabitat associations, possibly implying distinct local ecological interactions. These findings contribute to the assessment of stream conservation status and to recognize eventual direct impacts on fish structures along longitudinal gradients.
