In tropical estuaries, fish diversity varies spatially and temporally due to behavioral processes such as reproductive migrations, predator avoidance, and foraging, which are affected by water quality. Eutrophication is one of the main factors affecting water quality in estuaries. The objective of this study was to determine variation in fish assemblage explained by fluctuating water quality in the Buenaventura Bay. Fish were captured using artisanal trawl nets during the wet, dry, and transitional seasons at four sampling sites. Additionally, alkalinity; phosphate, nitrite, and nitrate concentrations; dissolved oxygen; pH; temperature; and suspended solids were measured. Multivariate analysis was used to assess the effect of water quality on fish assemblage. In Buenaventura Bay, the assemblage composition of Pseudupeneus grandisquamis, Daector dowi, and Citharichthys gilberti was affected by nitrate concentration. Moreover, large fish biomasses were associated with high nitrite concentration, intermediate salinity, and low dissolved oxygen, suggesting that these estuaries are dominated by species tolerant to poor water quality. Species richness was associated with low nitrate and phosphate concentrations, more suitable water quality indicators, and intermediate temperatures. These results suggest that the deteriorating water quality of estuaries as a result of the anthropogenic impact could increase dominance and decrease richness, resulting in structural changes of fish assemblages.