Alfacs and Fangar (North East of the Iberian Peninsula) are two embayments of the Ebre Delta complex with typical Mediterranean characteristics. Both are subject to the same meteorological forcing and receive similar freshwater inputs from irrigation drainage channels. However the basin volume in Alfacs is about ten times larger than in Fangar. We studied the temporal patterns of series of chlorophyll a and phytoplankton counts sampled between 1990 and 2003 from two depths of a fixed station in each bay, and related them to the variability of environmental variables (water, temperature, salinity and stratification). A principal component analysis performed on the correlation matrix among the (log-transformed) abundance data of the most frequent taxa revealed three main trends of variability. The first principal component (PC1) indicated a gradient of marine (more important in Alfacs) versus freshwater (particularly in Fangar) influence. PC2 reflected the seasonal cycle of phytoplankton in Alfacs, characterized by the dominance of a diatom assemblage typical of Mediterranean coastal waters in autumn and a group of dinoflagellates, including toxic taxa, in winter–early spring. PC3 expressed mainly the seasonal changes in Fangar and opposed a mixed phytoplankton group, including mostly dinoflagellates, with population maxima between May and October, to dinoflagellates of the winter group. Empirical Mode Decomposition was applied to the environmental variables and to the principal components in order to analyze the temporal structure of the data. All the series presented strong seasonal modes; an index based on phase shift between pairs of series revealed correlations between some of the principal components and environmental variables (temperature and salinity in Alfacs and temperature, salinity and stratification in Fangar). Water temperature showed a slight increasing trend along the sampling period. Between 1997 and 2003, some phytoplankton taxa also presented a weak increasing trend, particularly in the bottom samples of Fangar. This finding does not indicate a direct relationship between phytoplankton variability and the actual magnitudes of temperature or salinity. Rather, these environmental variables should be considered here as proxies of the seasonal behavior of a complex of environmental and biotic factors. Differences among the seasonal patterns of phytoplankton variability in Alfacs and Fangar could be attributed to the lower residence times of the water in Fangar, which resulted in a stronger hydrological control of phytoplankton abundance and composition.