The response of coastal lagoon plankton communities to warming was studied during two in situ mesocosm experiments in spring and fall of 2018 in the Mediterranean. Phytoplankton biomass, gross primary production (GPP), community respiration (R), phytoplankton growth (µ), and loss (l) rates were estimated using high-frequency chlorophyll-a fluorescence and dissolved oxygen sensors, and daily sampling was used to evaluate the nutrient status and phytoplankton pigment functional groups. Warming strongly depressed the dominant phytoplankton functional groups, mainly the prymnesiophytes, diatoms (spring), and green flagellates (fall). It favored minor groups such as the dinoflagellates (spring) and diatoms (fall). In spring, warming depressed GPP and R by half; however, µ (+ 18%) and l (+ 37%) were enhanced. In contrast, both GPP and µ were enhanced by 21% and 28%, respectively, in fall, and no effects were observed for R and l. Warming strongly decreased phytoplankton biomass and oxygen production in spring, and enhanced them, to a lesser extent, in fall. This led to an overall loss of production over both seasons. This study improves understanding of the contrasting effects of warming during two productive seasons, which depend on plankton community composition and interactions between components and environmental conditions.