While substantial progress has been made in evaluating the ecological carrying capacity (ECC) for fish farming in temperate regions, studies in tropical environment remain scarce, and benthic ecological thresholds are still lacking. This study combines spatial measurements of waste deposition (quantified with sediment traps and depositional modelling approaches), with measurements of sediment physical and biogeochemical properties and macrobenthic community structure at a shallow, non-dispersive site in Martinique. Despite minimal changes in sediment physical and biogeochemical properties, pronounced effects were observed on macrobenthic communities structure. At farm sites, benthic communities were highly perturbed (extremely low diversity and abundance of individuals) and dominated by few individuals of second-order opportunistic species. At sites located between 25 and 150 m from the farm, benthic communities were similar and characterised by higher diversity and abundance, with the presence of sensitive species to OM enrichment. The benthic response was strongly driven by organic waste deposition, which was elevated directly beneath and adjacent to the fish cages. The benthic response to depositional fluxes was best described by M-AMBI index. Notably, the transition from ‘Moderate’ to ‘Poor’ ecological status occurred within a depositional range of 1.2–3.0 kg m−2 year−1 for POM and 0.6–1.1 kg m−2 year−1 for TOC, with model predictions suggesting that these effects may extend up to 30 m from the farm. This study represents a step forward in defining benthic ecological thresholds for tropical fish farming and will help decision makers in fostering the sustainable development of aquaculture in these regions.