A 10 yr study was carried out in the Tremiti Archipelago, a multiple-use Marine Protected Area (MPA) several miles off the mainland (South Adriatic, Italy), with a very small and isolated no-take area established in 1989 and characterized by limited enforcement. Patterns of variation in benthic assemblages along the intertidal rocky shores and in the rocky subtidal inside and outside the no-take area were examined between 2001 and 2010. Remarkable changes in the intertidal assemblages were detected within the no-take area, with an increase of Cystoseira canopies and the development of more diversified understory assemblages through time. Signs of regression in Cystoseira were documented in unprotected control areas. Conversely, < 20 yr after the MPA designation, bare rock and patches of crustose coralline algae characterized subtidal assemblages in the no-take area. Increasing spatial heterogeneity of both intertidal and subtidal assemblages, probably representing an early warning of increasing human pressure, was also assessed. Data on primary production showed significantly higher values in the control areas than in the no-take area, with increasing values over time, indicating that the observed patterns are triggered by a combination of different drivers. Our results suggest that: (1) the effects of protection over benthic assemblages greatly depend on the habitats considered, which in turn, respond differently to specific human pressures occurring within and outside the reserve. A careful analysis of the distribution and intensity of all the activities allowed within multiple-use MPAs is critical for improving the effectiveness of conservation actions. (2) Isolation per se does not guarantee exclusion from human activities. In the presence of low enforcement, isolation may play a limited role in mitigating human pressures on benthic assemblages and may impair the connectivity of reserve networks.