In recent decades marine reserves have been established throughout the world as a management tool for compensating the effects of overfishing on coastal marine stocks. Despite the growing literature about the expected response of populations and communities to protection from fisheries, and the number of studies measuring some of these effects, most of the mechanisms supposed to work in a marine reserve have not yet been empirically demonstrated. One of the main difficulties ecologists have to face when approaching this problem is the inherent spatial and temporal heterogeneity of ecosystems. This paper reviews the relevant literature and addresses the influence of physical environment (or habitat structure) on ecological processes occurring at the individual, population, and community / ecosystem levels of organization. It evaluates how the responses confound the ``reserve effect'' with some aspect of the ``habitat effect''. Finally, it proposes some practical considerations for improving the methods aiming to evaluate the effect of protection in the face of heterogeneity, illustrated with some examples taken from our studies on Mediterranean rocky reef fish assemblages, and argues that a multiscaled, hierarchical approach to this problem (the seascape perspective) should be adopted as an integrating principle when designing a research program aiming to understand the way marine reserves work as fisheries management tools.