Coastal marine assemblages are shaped by interactions between physical factors, biological interactions, and almost ubiquitously, human impacts. Large-scale manipulations of human access replicated over a range of physical and biological conditions can generate insights over the processes shaping marine assemblages. We examined the relative roles of human impacts and hydrographic conditions on assemblages of shallow (3-10 m depth) rocky reefs by comparing no-take reserves with fishing areas occurring in gradients of exposure of the coastline to dominant winds and waves around two Mediterranean islands, Capraia and Giannutri, Italy. We hypothesized that fishing influences assemblages directly by reducing populations of target fish species, and indirectly by reducing predation on sea urchins, intensifying herbivory, and causing ''barrens'' of encrusting coralline algae. We examined how the possible effects of fishing varied with physical exposure of the coastline.The composition of fish assemblages differed significantly between sites within no-take reserves and fished reference sites. Abundances and sizes of predatory fishes targeted by local fisheries were greater in no-take reserves than in fished areas. Sea urchin densities, the extent of coralline barrens, and the structure of the algal and invertebrate benthic assemblages showed clear variation associated with exposure of the coastline to dominant winds and waves, but weak effects of protection from human use. Densities of the black sea urchin Arbacia lixula were significantly greater along the windward than along the leeward sides of the islands, and were positively correlated with the extent of coralline barrens. In contrast, the purple sea urchin Paracentrotus lividus was more abundant along the leeward sides of islands and showed indirect responses to protection at Giannutri, where purple sea urchins tended to have greater densities at fished than at protected sites. Protection from fishing influenced fish assemblages directly, and benthic assemblages indirectly, but the latter effect was observed only at sites with lower physical exposure. Indirect effects of fishing and recovery of assemblages within marine protected areas through cascading trophic interactions are likely to vary depending on local physical conditions and on the characteristics of species that are locally dominant.