Short-term bioassays were conducted in Biguglia lagoon (Corsica) to study the physiological and behavioral responses of phytoplankton to N- and P-availability. Natural communities were collected in two stations representative of the two sub-basins, at three periods with contrasting environmental characteristics to address the impact of seasonal variability. These samples were separately enriched with a full N and P enrichment, and with enrichments minus N or minus P. Phytoplankton size structuration, diversity, and growth of the total phytoplankton, the micro-, nano- and ultraphytoplankton were evaluated using spectrofluorimetry, and optical microscopy. Results showed that the communities were fueled by NO3− in the wet periods (autumn and spring) and NH4+ in summer. The phytoplankton communities displayed highest cell size in autumn, with high abundances of nanoflagellates, and smallest cell size in summer with a large dominance of phycocyanin-rich picocyanobacteria. Blooms of dinoflagellates also occurred during the wet periods, coinciding with high N:P ratios. The full enrichment has not stimulated phytoplankton growth in autumn, suggesting the importance of other controlling factors such as light, a possible NH4+ inhibition or the use of mixotrophic abilities. In spring, communities have displayed single P-limitation in the northern basin and different N and P co-limitations in the southern basin. In summer, the full enrichment consistently stimulated the growth of all cell sizes. The communities showed high N and P co-limitations, which is consistent with growing observations in aquatic ecosystems, and reflects the different functional responses of phytoplankton communities to the nutrient availability.