We explored the role of natural and anthropogenic environmental perturbations in shaping the community structure and dynamics of pico- and nanophytoplankton in coastal waters. The distribution patterns of phycoerythrin-rich picocyanobacteria (PE-CYAN) and phycocyanin-rich picocyanobacteria (PC-CYAN), autotrophic picoeukaryotes (PEUK) and nanophytoplankton (NANO) were examined over a period of 3 yr in 24 Mediterranean coastal lagoons displaying wide trophic gradients (from 0.2 to 630 mu g chlorophyll a [chl a] l(-1)) and salinity gradients (from fresh to marine waters). In summer, picoplanktonic abundances reached 3 x 10(8) cells l(-1), 5 x 10(9) cells l(-1) and 6 x 10(10) cells l(-1) for PE-CYAN, PC-CYAN and PEUK, respectively. PE-CYAN and PC-CYAN showed opposing responses to environmental gradients, resulting in a restricted dominance of PE-CYAN in oligotrophic marine lagoons and a dominance of PC-CYAN in some eutrophic brackish lagoons. Most lagoons exhibited steady-state nutrient conditions, giving competitive advantages to small eukaryotic algae, even in eutrophic and hypertrophic waters. Among the picophytoplankton, picoeukaryotes (ca. 2 to 3 mu m) are the most competitive with increasing nutrient availability; in terms of abundance and biomass, their relative and absolute importance tended to increase with increasing total chl a biomass. Freshwater discharges resulted in large pulses of nutrient and more turbulent systems that altered the structure of the phytoplankton community and stimulated fast-growing NANO composed of phytoflagellates and diatoms (ca. 3 to 6 mu m, up to 1.6 x 10(9) cells l(-1)). Members of the microphytoplankton (ca. 20 to 200 mu m) were rarely observed in eutrophic and hypertrophic lagoons and were composed of harmful dinoflagellates in oligotrophic lagoons. These results show that anthropogenic and meteorological changes are highly influential on the composition and size structure of phytoplankton communities.