Water quality regulations involve a significant commitment of resources by both governments and private entities. It is essential to continuously evaluate the effectiveness of these regulations to ensure that they meet the expected impact. In this study, nutrient data were analyzed as indicators of primary productivity, together with dissolved oxygen (DO) concentrations and pH as response variables, to evaluate historical trends in water quality in 55 stations in Puerto Rico. The stations were categorized as affected and unaffected according to their historical average concentration of total phosphorus (TF). The average concentrations of FT and total nitrogen (NT) were significantly higher in the affected seasons compared to the unaffected ones. In contrast, the average DO concentrations and the average pH values were significantly lower in the affected seasons. A generalized additive model with mixed effects was used to analyze temporal trends. In the affected seasons, a significant decrease in FT and NT concentrations was observed over time, accompanied by significant increases in DO and pH concentrations. The unaffected stations showed a marginal and statistically insignificant downward trend. The notable nutrient reductions observed in the affected seasons appear to be related to the closure of several major wastewater treatment plants (PTAR) on the island. The conversion of abandoned agricultural land into secondary forests over the past few decades has caused small but significant decreases in NT (not FT) in receiving streams. We conclude that the Clean Water Act has promoted improvements in water quality in Puerto Rico by promoting the modernization of health infrastructure and the regulation of specific sources of pollution.