Beta diversity helps to understand changes in species composition over space and time, with two key components: nestedness (hierarchical pattern in richer sites) and turnover (species replacement due to niche or dispersal differences). It measures the loss or gain of species (nestedness) and species replacement (turnover) when comparing two or more spatial/temporal/environmental units. As both components require different species conservation strategies, assessing which of them the communities are organized is an important tool for this purpose. Our study aimed to evaluate which two components of beta diversity (nestedness or turnover) are responsible for structuring invertebrate and fish assemblages on the southern coast of Brazil. This region is historically recognized as a shrimp trawling area, a type of fishing with negative impacts on marine biota, such as the removal of species and habitat destruction. Our results suggest that the overall beta diversity values demonstrated a high environmental heterogeneity among the sampled areas. The most significant fraction of the general beta diversity for both assemblages is explained by the spatial turnover component. As depth increased, there was a significant rise in overall beta diversity and species turnover for fish and invertebrate assemblages. In contrast, there were no significant correlations among the nestedness component, the geographical distance and depth. In water mass conditions, fish assemblage decreased with rising chlorophyll and decreasing temperature. Elevated marine phosphate and thick sediments adversely impacted invertebrate composition. Additionally, invertebrate richness showed a positive correlation with fine sand grains. The research conducted along the southern coast of Brazil suggests the utmost importance of these regions in terms of species conservation. Here, the dominant influence of the turnover component shapes the organization of subtropical marine benthic assemblages. Furthermore, these areas receive frequent visits from migratory species, further accentuating their ecological significance.