The Júcar River flows into Cullera Bay in the western Mediterranean Sea (Valencia, Spain). The river flow is over-exploited and usually has no significant discharge at the mouth, except during very rainy periods. As part of the ECOSUD project, nine sampling campaigns were carried out (June 2002–July 2003) at different stations and depths in the Júcar Estuary and Cullera Bay. This paper presents the nutrient analyses of two campaigns (summer and spring) with different weather conditions (without and with freshwater flow respectively). The results show that the freshwater layer of the river was higher in the spring campaign (April) than in the summer campaign (July), which resulted in a more evident freshwater influence at the marine stations near the river mouth. As expected, there was a general downward trend in the dissolved nutrient concentrations with lower river flow (lower continental influence). However, the variations observed were not always linear. With some exceptions, nutrient concentrations generally increased. Ammonium, SRP and orthosilicic acid increased due to the senescence, death and subsequent mineralization of freshwater organisms as salinity increased. Nitrate and nitrite also increased somewhat due to the nitrification of the ammonium. However, nitrite showed some losses in summer conditions (July) related to the different speeds of the two nitrification steps.