The impact of changes in nitrogen (N) and phosphorus (P) availability on the trophic strategies of planktonic protists was evaluated in a disturbed Mediterranean lagoon (Biguglia lagoon, France) using short-term bioassays. Natural communities were collected in three periods, i.e., autumn, spring and summer, to address the influence of the different environmental conditions. The responses of autotrophic plankton communities to experimentally induced N and/or P limitations were assessed as changes in chlorophyll a (Chl a) concentrations and in the abundances of potentially mixotrophic protists taxa. We observed blooms (> 105 cells l−1) of nanoflagellates in autumn, and of phycocyanin-rich picocyanobacteria in summer. Communities showed a co-limitation by N and P at the three sampling periods, despite high N:P ratios in autumn and spring. The high abundances of potentially mixotrophic dinoflagellates during these periods suggest the involvement of alternative trophic pathways for their maintenance in the lagoon. After bioassay incubations using different nutrient enrichment treatments, we often observed reduced abundances of mixotrophic protists containing Chl a with a concomitant increased abundance of protists without Chl a. This indicates a loss of chloroplasts and photoautotrophic abilities in protists cells, possibly reflecting a shift towards heterotrophy that could be sustained by phagotrophy.