The present study proposes a diagnosis of water quality and fishery production in the Estuarine Complex of Santos, São Vicente, and Bertioga Cities as a requirement for economic valuation of water pollution impacts on fishing production. In the study period (2009–2014), three water quality parameters were identified (dissolved oxygen, total phosphorus, and nitrate), which occurred more frequently in non-conformity with Brazilian water standards, according to reports released by the Environmental Company of São Paulo State (Companhia Ambiental do Estado de São Paulo — CETESB). For data collection of fishery production, data from the monitoring of Institute of Fisheries of Santos City (Instituto de Pesca de Santos) were used, and 15 species were identified with higher occurrence in the study area. The relation between water quality parameters and fishery production was analyzed with mixed linear models, in which significant values for dissolved oxygen parameters, total phosphorus (positive relation), and nitrate (negative relation) were found. Environmental valuation considered only the direct use values (DUV) component of the valuation of fishery production variation in relation to water quality variation. For this purpose, the Marginal Productivity Method (MPM) of the dose-response function was used, which resulted in a range of monetary loss between US$ 24,760,550.22 and US$ 60,635,978.78. The obtained values represent only a portion of the valuation of economic and environmental loss in the fishing activity (part of DUV). Therefore, economic value calculated is conservative, and although it did not reached the total amount corresponding to all the impacts caused by poor water quality, given the limitations of methods and study period, the obtained values represent the minimum environmental monetary loss.