In this article, the floristic lists and the seasonal mean cell volumes of phytoplankton taxa observed in three Mediterranean lagoons are reported. These datasets include 40 species, 67 other taxa identified at least at genus level, and further 13 taxa attributed only at order or class level. These data are associated with Pulina et al. "Seasonal variations of phytoplankton size structure in relation to environmental variables in three Mediterranean shallow coastal lagoons" (Pulina et al., 2018) [1], where phytoplankton taxa were included in two different cell size classes (Utermöhl fraction of phytoplankton, cell size > 3 µm; Picophytoplankton, cell size < 3 µm) and in which their seasonal variations were interpreted and discussed.