Quantifying scale-dependent patterns and linking ecological to environmental variation is required to understand mechanisms regulating biodiversity. We conducted a large-scale survey in rocky shores along the SE Brazilian coast to examine spatial variability in body size and density of an intertidal barnacle (Chthamalus bisinuatus) and its relationships with benthic and oceanographic predictors. Both the size and density of barnacles showed most variation at the smallest spatial scales. On average, barnacle body size was larger on shores located in areas characterised by higher chlorophyll levels, colder waters, low wave action and low influence of freshwater. Barnacles were more abundant at wave-exposed shores. We identified critical scales of spatial variation of an important species and linked population patterns to essential environmental predictors. Our results show that populations of this barnacle are coupled to scale-dependent oceanographic variation. This study offers insights into the mechanisms regulating coastal populations along a little studied coastline.