We conducted a mesocosm study to investigate the combined effect of organic enrichment and sediment resuspension by shrimp on phytoplankton communities in shrimp aquaculture ponds. Hence, the factorial design included two factors, i.e., (i) shrimp density with a concomitant increase of feed input resulting in organic enrichment and (ii) with/without access of shrimp to the sediments. Increasing feed input in the system raised the eutrophication state of the environment characterized by an increase in phytoplankton biomass. Bioturbation enhanced (i) mineralization of organic matter via the microbial loop, resulting in faster nutrient recycling, (ii) an increase of primary production, and (iii) buffering capacity against eutrophication consequences. The phytoplankton community showed both large temporal variations of its taxonomic composition and resilience to treatments. A shift in species dominance from Diatoms + Dinoflagellates to green algae was observed in all treatments and coincided with meteorological and N pool changes. Results suggested that algal production was primarily limited by phosphorus and light at low (i.e. low feeding) and high (i.e. high feeding) eutrophication states, respectively. Growth rate appeared as an important factor of dominance in this highly dynamic ecosystem. Consequences for water column management are discussed.