Coastal habitats are critical transition zones supporting a diverse and abundant marine community but are under strong human influence. Sustainable management of those habitats must rely on robust understanding of the processes regulating the diversity and functioning of the local communities. However, most of the studies to date have focused predominantly on the benthic communities from positive surface of rocks. Here, using a sessile community from negative surfaces, we described how larval availability, recruitment, predation and physical parameters affect the diversity and distribution of species along a gradient formed from the mouth to the middle portions of a diverse coastal bay threatened by the expansion of a port in the Southwestern Atlantic Ocean. Monthly, from August 2015 to November 2016, we compared the composition of sessile species on the lateral and undersurface of rocks, the water physical parameters, the substrate composition and availability, as well as the abundance of larvae in the plankton and the recruitment in the mouth and the middle portions of the bay. Additionally, we also conducted a predator exclusion experiment to compare the predation pressure across the bay. The sessile community in the middle of the bay is a subset of the community in the mouth, where ascidians and bryozoans contributed to increase diversity. While the amount of rocky substrate was similar between sites, the proportion of granite, the water turbidity and the chlorophyll concentration were higher in the middle of the bay. Larvae and recruits were more abundant in the middle of the bay, mainly during the spring and summer months, but recruits were more diverse in the mouth of the bay during the whole study. Although reducing diversity, predation had similar effects in the two sites and did not explain the differences in the sessile communities. Our results reinforce that in critical transition zones, the relative importance of regional oceanic and local processes changes along the ocean-land gradient. While communities in the mouth of the bay are more diverse and dynamic, being composed by several species of colonial filter-feeding organisms, the high turbidity in the middle of the bay seems to restrict those organisms, resulting in communities mainly composed by serpulid worms and oysters. Communities closer to the bottom of the bay are also near to the source of allochthonous sediments and nutrients, being consequently more susceptible to human disturbances.