Understanding the multiplicity of processes producing genetic patterns in natural populations can shed light on the ecology and evolution of species, and help guide effective management and conservation strategies. Here we investigated the role of environmental, demographic, and geographic factors in shaping the spatial patterns of genetic diversity and differentiation of the intertidal barnacle Notochthamalus scabrosus along the central-northern coast of Chile (28−34° S). We analyzed genetic data from 7 microsatellite loci genotyped for 300 individuals sampled from 10 sites and combined this information with 8 site-specific environmental (4), demographic (2), and geographic (2) variables using least squares linear regressions, generalized linear models, and matrix regression analyses. We found a strong association between the spatially structured genetic diversity of N. scabrosus and patterns of temporal variability in chlorophyll a, and among-site differences in seawater temperature and adult abundance. Our results illustrate that population size, partly driven by recruitment success, can leave a signal on genetic structure of this highly dispersive marine species. The significant effect of temperature and chlorophyll a stresses that local adaptation may be key to understanding the spatial genetic structure of our model species. Hence, the results of this work represent an advance towards understanding the usually complex causal relationships between environmental variables, gene flow, and genetic diversity patterns of coastal populations.