At Ensenada de La Paz, a coastal lagoon on the western side of the Gulf of California, nutrient and salinity data before and after rain events were evaluated using a mass balance model to estimate the exchange of conservative and non-conservative variables with the adjacent sea. Surface salinity, nitrogen (N-NO3, N-NO2), and phosphorus (PO4) were used in the model to obtain the hydraulic balance, water residence time, and nitrogen and phosphorus fluxes. Results showed that residual volume was mainly influenced by evaporation. Rainfall and runoff increased the mixed volume and reduced water residence time. Pre-rainfall hydraulic balance conditions were reestablished about 10 days after a rain storm. Rainwater inputs also modified the quality of the coastal lagoon: the pre-rainfall scenario showed that more nitrogen is consumed than produced, and there is a phosphorus sufficiency. A rain disturbance induces a nitrogen and phosphorus increase. Eleven days after a rain storm, nitrogen and phosphorus levels did not return to the pre-rainfall scenario. Rain disturbances in arid zone coastal lagoons modify their water quality and exchange with the adjacent ocean; some management strategies are suggested.