Metacommunity theory addresses local interactions and regional processes, offering a powerful framework to comprehend the species composition of a region and the factors that shape its structure along environmental gradients. By incorporating spatial dynamics, the metacommunity analysis explores the relationships that govern the ecological communities at different spatial scales. The objective of this work is to describe the structure of a metacommunity of living foraminifera, to relate it to physical and chemical variables of water and sediment, and to identify the environmental characteristics associated to the assemblages. A total of 534,416 living foraminifera, belonging to 65 species, were collected at 106 stations across five tropical urban coastal lagoons along the coast of the Rio de Janeiro State (Brazil), subjected to a strong salinity gradient. The results of the Elements of Metacommunity Structure (EMS) analysis identified four distinct assemblages of living foraminifera across the lagoonal systems. These metacommunities fitted a quasi-nested pattern, with the total variation explained by a shared influence of environmental factors (primarily hydrological drivers associated with marine influence, such as salinity, pH, and temperature) and spatial predictors. Organic enrichment descriptors (TOC, TS, CHO, PTN, LIP) played a secondary role in the ordination of the sites. The findings of this work demonstrate the potential of the EMS approach as a valuable tool for establishing a baseline in environmental monitoring plans.