The hydrological characteristics and the rate of organic matter supply from coastal lagoons help to understand their responses to nutrient input by anthropogenic and natural sources. The aim of this study was to determine the hydrologic and trophic status of the El Rancho-Empalme lagoon system in a semiarid region in the Gulf of California, Mexico. This lagoon system consists of two geomorphological subsystems which are affected by nutrient inputs from shrimp farm effluents and coastal upwelling. Sampling was conducted over the course of one year and included measurements of temperature, salinity, and dissolved oxygen, surface water grab samples to analyze nitrite, nitrate, ammonia, orthophosphate, and chlorophyll