The study of larval dispersal and connectivity between deep-sea populations is essential for the effective conservation and management of deep-sea environments and the design and implementation of Marine Protected Areas. Dense sponge aggregations, known as “sponge grounds”, are a key component of marine benthic ecosystems, by increasing the structural complexity of the sea floor and providing structure and habitat for many other species. These aggregations are characteristic of the Azores deep-sea environment. These sessile organisms rely primarily on larval dispersal for their reproduction. Connectivity between specific Pheronema carpenteri sponge aggregations in the Azores was studied using a 3-D biophysical dispersal model. Different biological trait scenarios were analyzed, considering spawning seasonality and pelagic larval duration. Model results indicate that regional circulation patterns drive larval dispersion, shaping population connectivity of P. carpenteri sponge aggregations in the Azores, particularly among aggregations in the Central Group of Azorean islands. Some areas present high retention rates, receiving larvae from several sponge aggregations while also being important larval source aggregations. In contrast, aggregations from the Eastern Group may be isolated from the others. Larval dispersal and connectivity patterns were analyzed concerning the current configuration of Marine Protected Areas (MPAs) in the Azores. The results underscored the importance of maintaining protection efforts in existing MPAs and identified stepping-stone locations and specific sites where additional measures could enhance species connectivity in the Azores.