Nutrients, particularly nitrogen and phosphorus, are widely used in agricultural activities worldwide, but the excess of these elements can significantly impact marine ecosystems. La Ventana Bay is a coastal zone surrounded by agriculture and other anthropogenic activities (formerly a mining area). It also has the presence of important geological faults, which cause hydrothermal activity on the beach and groundwater of the valley. This study evaluated nitrogenous nutrients (N-NO2-, N-NO3-, and N-NH4+) and phosphate contamination levels in groundwater (Los Planes aquifer) and seawater (La Ventana Bay). The objective was to confirm possible nutrient sources and determine their transport through groundwater towards the bay. Field sampling was conducted in three climatic seasons. Dissolved concentrations of the N and P chemical species were analyzed in marine water and groundwater samples. Results indicate that during the dry, and cool rainy seasons, a higher nutrient input was observed in the north of the bay, where the submarine groundwater discharge (SGD) was identified. This confirms the importance of the SGD as a pollutant source for the bay and suggests that nutrient transport from agricultural sources is seasonally variable, with potential implications for coastal ecosystem dynamics. This study highlights groundwater as a key transport pathway of nutrients from agricultural areas to coastal ecosystems, emphasizing the need for monitoring strategies to mitigate eutrophication risks.