This paper presents the results of phytoplankton counts carried out with epifluorescence at five sampling stations: two in the Júcar River Estuary and the other three in the region of freshwater influence of the Júcar River. From June 2002 to July 2003, nine sampling campaigns were carried out as a part of the EU's ECOSUD project. Two of these campaigns (the 2nd and 8th) were selected for analysis. These sampling campaigns represent two different conditions: in the 2nd campaign the discharge of the Júcar River was almost null, while in the 8th campaign it was significantly higher.

Along the salinity gradient, as the influence of fresh water and nutrient loads decreases, a decrease in the population density of eukaryotic phytoplankton was observed. Typical freshwater phytoplankton groups (colonial cyanobacteria and chlorophyceae) clearly decrease in density and percentage as salinity increases. In general, picocyanobacteria exhibit the opposite behavior. The behavior pattern of groups with species adapted to fresh water and seawater is less clear. The density of these groups (diatoms and prymnesiophytes) is highest in the salt-wedge area due to nutrient accumulation. However, the densities are generally higher at the freshwater stations than in the marine environment. The vertical distribution at the estuarine stations shows clear density maximums in the interface area, which seems to have two causes: the retention of senescent phytoplankton affected by saline shock in this quiescent area and the growth of phytoplankton that exploit the accumulated nutrients.