A basic input for implementing ecosystem-based management measures is the knowledge on fish assemblages exploited by multispecies fisheries, such as the set gill net artisanal fishery in the Gulf of Salamanca (GoS), Caribbean Sea (Colombia), which catches a large number of high-value demersal species. Assemblages of this type were identified in this study, and significant differences (P < 0.01) between sampling periods (2008 and 2013) and seasons were found by means of a two-way permutational multivariate analysis of variance. These results were consistent with those obtained with the principal coordinates analysis, indicating the occurrence of short-term structural changes in these assemblages. Interannual and seasonal variations in discriminant and typifying species were also identified using similarity percentages, and a decreasing trend in landing per unit effort was established by the bootstrap method. On the other hand, both the geographic location of the fishing grounds and the characterization of historical changes in the set gill nets used in the GoS were determined using the traditional ecological knowledge of local fishermen, who reported a decrease in mesh sizes. In conclusion, temporal variations could be related to changes in the gill nets, the fishing trip schedules, and the spatial distribution of fishing effort, all which occurred in response to the decrease in catch rates in traditional fishing grounds.