The East Continental Shelf (ECS) of Brazil is a hotspot of endemism and biodiversity of reef biota in the South Atlantic, hosting a number of Marine Protected Areas (MPAs). Connectivity of MPAs through larval dispersal influences recruitment, population dynamics, genetic structure and biogeography in coral reef ecosystems. Connectivity of protected reef ecosystem in the ECS was investigated with a hydrodynamic model (ROMS) forcing an Individual Based Model (IBM—Ichthyop), and used groupers (genus Mycteroperca) as functional group. The hydrodynamic output from ROMS was compared with satellite data and showed good agreement with observed surface fields. Eggs were released, in IBM experiments, from April to September along six years (2002–2007) in five MPAs along the ECS. Intrannual variability in recruitment and self-recruitment of grouper larvae was observed, as well as a negative correlation of these population parameters with total Kinetic Energy (KE) used as a metric of the physical environment. Higher KE leads to increased offshore advection of larvae, reduced total recruitment and connectivity of MPAs. Our results indicate high and uni-directional connectivity between MPAs from north to south influenced by the Brazil Current flowing in the same direction. Results also showed that some MPAs act predominantly as “sink” while others are mainly “source” areas.