The Júcar River, characterized by a very irregular freshwater flow, discharges into the Spanish Mediterranean coastal waters. However, the flow at its mouth is usually insignificant due to the overexploitation of upstream water. Under normal conditions, the final stretch of the river (downstream from the Cullera weir) is nurtured only by water released from the weir and small discharges from lateral irrigation channels. During periods of heavy rain, however, a significant amount of water flows through the Cullera weir. An analysis of data acquired during several field campaigns in Cullera Bay clearly reveals a zonal distribution of nutrients and chlorophyll-a within the bay: a southern area of continental influence, located near the mouth of the Júcar River; a region affected by karst filtrations and minor freshwater inputs, located to the north of the bay around Cullera Cape; and a third zone in between, characterized by higher salinities. Spatial salinity distribution is indicative of the spatial distribution of some of the nutrients discharged by the river, particularly nitrite, nitrate, orthosilicic acid and total phosphorus (TP), since it has been shown that their behavior is inverse to that of salinity. However, neither soluble reactive phosphorus (SRP) nor ammonium, which are mainly affected by biological activity, show this type of behavior. Five different conditions/scenarios were identified during the overall sampling period based on the time-series analysis of wind parameters, rainfall, freshwater flow, salt-wedge thickness at the measuring station on the river, and by comparing the average surface salinity at the sea stations with the values obtained at the coastal stations.