The Cullera Estany is a coastal lagoon located in a highly intensified agriculture and tourist area in Valencia. This coastal lagoon has connections with the sea that produce marine intrusion and generate a freshwater interface. Four sampling campaigns were carried out during 2010 in order to analyse the phytoplankton composition and its relation to nutrient content through a Redundancy Analysis. Temperature, dissolved oxygen, nitrite and salinity are the main factors controlling the dynamics of phytoplankton community. During July and October, there is water column stratification; meanwhile in March, there is a well-mixed water column. In addition, in May and July campaigns, hypoxia/anoxia conditions are detected at the bottom. The most abundant phytoplankton groups are Diatoms and Cryptophyceae. Diatoms and Cyanophyceae respond positively to temperature while Cryptophyceae, Prasinophyceae and Dinophyceae respond to high salinity and dissolved oxygen values. Furthermore, picoplankton is correlated inversely with nutrient concentrations.