Soft-sediment benthic habitats are shaped by interactions between physical forcing and biological processes, yet their relative roles in low-disturbance remain unclear. We tested whether hydrodynamic regime acts as a primary driver of taxonomic and functional structure across a depth gradient (20–70 m) in Nuevo Gulf, a trawl-free marine protected area in northern Patagonia. Between April 2023 and February 2024, 601 non-destructive video quadrats, covering a total area of 1012.6 m2 were collected using the towed quadrat system Toki in zones of contrasting tidal current intensity. Hydrodynamic regimes were validated through in situ measurements and Regional Ocean Modelling System outputs. Assemblage structure was analyzed using richness estimators, PERMANOVA, nMDS ordination, indicator species analysis, and species co-occurrence networks. Thirty-five taxa of benthic organism were recorded. High-current environments supported higher cumulative richness, greater evenness, and assemblages dominated by suspension feeders and structure-forming taxa. In contrast, low-current areas were strongly dominated by the squat lobster Grimothea gregaria (~85% of total abundance), resulting in reduced evenness and simplified association patterns. Both the current regime and depth significantly influenced community composition, with hydrodynamic effects intensifying at greater depths. Network analyses revealed higher connectivity and recurrent positive associations under high-current conditions, consistent with increased structural complexity and functional integration. Our results demonstrate that hydrodynamic forcing modulates depth-related patterns and governs both composition and species associations in temperate sublittoral soft sediments, providing a robust ecological baseline for predictive habitat mapping and conservation planning in the southwestern Atlantic.