Seagrass beds are highly productive coastal ecosystems that sustain a rich and diverse associated fauna and flora. Increasing anthropogenic pressures threaten seagrass ecosystems and have already led to major seagrass losses across the world. Marine Protected Areas (MPAs) have become one of the key strategies to manage coastal ecosystems and associated resources worldwide and have been often shown to successfully protect marine ecosystems. However, relatively few studies have assessed the effects of MPAs on seagrass ecosystems, and there are indications that MPAs may not be able to fully protect seagrasses, especially from disturbances originating outside their boundaries. Within this context, this thesis aimed to investigate the direct and indirect effects (those mediated by biotic interactions) of MPAs on tropical seagrasses, associated fish communities, and ecosystem processes.

The thesis consists of three parts. First, we used 10-years of seagrass monitoring data within a MPA to evaluate the temporal variability in seagrass cover and species composition in relation to changes in environmental conditions (Paper I). Second, we investigated the potential of MPAs to enhance the temporal stability of seagrass ecosystems using a 10-month field study. We surveyed seagrass-associated fish communities (Paper II) and estimated seagrass growth and herbivory rates (Paper III) during three different seasons within MPAs and unprotected sites. Finally, to evaluate the effects of MPAs and land-use on seagrass ecosystems we surveyed seagrass species and trait composition within government-managed MPAs, community-managed MPAs, and unprotected sites (Paper IV).

The seagrass bed monitored in Paper I showed a high temporal and spatial variability, with a temporal decline in cover and change in species composition, followed by a period of recovery. This pattern could not be associated with any of the climate and tidal variables considered, suggesting that potential drivers of decline may have originated outside MPA boundaries. The results from the seasonal field study showed that MPAs increased the temporal stability of seagrass-associated fish communities, particularly juvenile fish (Paper II), and strengthened a positive link between herbivorous fish, herbivory rates, and seagrass growth (Paper III), suggesting the presence of a positive feedback that promotes stability. Finally, MPAs affected seagrass species and trait composition (by selecting for more stress-sensitive species) but did not seem to be able to protect seagrasses from land-use effects, with seagrasses showing similar changes in species and trait composition within and outside MPAs (Paper IV). Considering these results, this thesis builds to a body of literature indicating that MPAs alone may not be sufficient to protect seagrass ecosystems and that improved management strategies may be necessary to preserve these important coastal habitats.