In marine environment phytoplankton and picoplankton are responsible for a bulk of production and nutrient cycling and may give important information about the different seawater habitats. In the present paper, the temporal changes of phytoplankton as well as autotrophic and heterotrophic picoplankton abundance and biomass in two coastal areas in the Gulf of Taranto (Mediterranean Sea) subjected to different levels of anthropogenic pressure were studied and related to the main environmental variables. The two analysed areas were significantly different as regards the abiotic conditions which also varied temporally. Univariate analyses revealed that larger phytoplankton and heterotrophic picoplankton abundance and biomass varied as well. The multivariate analyses showed a complex distribution of the whole planktonic assemblages, which varied in time and space without a decipherable pattern, presumably due to the peculiar spatial-temporal dynamics of the sole autotrophic picoplankton abundance. Significant correlations between planktonic assemblages and environmental variables were discussed by taking into account also the potential role of the considered planktonic components as useful environmental monitoring parameters.