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The richness and biomass distribution of mangrove macroalgae were evaluated along the main salinity gradient of the Paranaguá Bay subtropical estuarine complex in southern Brazil. We used a spatially hierarchical design to investigate the spatial scales that contributed most to the variation in richness and biomass within the association. A total of eighteen taxa of macroalgae and cyanobacteria were identified with nonlinear patterns of distribution. While richness correlated with the salinity gradient, algal biomass did not follow the predicted pattern. Conversely, most of the mangrove macroalgae distribution patterns were more related to small-scale processes than to salinity variation. These results indicated that even though coastal regions are exposed to large-scale environmental processes, the somewhat disregarded small-scale processes should be also considered to unravel patterns in biological distributions.