Optimal water quality is a prerequisite for the economic and environmental sustainability of shrimp aquaculture. The dynamics and succession of phytoplankton and microzooplankton assemblages and their interrelationship with water-quality parameters in 2 commercial ponds growing whiteleg shrimp Litopenaeus vannamei in southwestern coastal India were assessed through periodic sampling during 96 d of culture. Of the many centric diatoms that were encountered during the initial stages of culture in nitrogen-rich conditions, only 2 dominant species, both belonging to Thalassiosira, persisted throughout the progression of the culture to produce a healthy bloom (up to 6 × 10 6 cells l −1). Blooms of Thalassiosira spp. contributed significantly to the in creased phytoplankton biomass towards the end of culture period, with a concomitant decrease in concentrations of ammonia and nitrate. The succession of pennate diatoms such as Nitzschia closterium, Pleurosigma elongatum and Thalassionema nitzschioides in moderate abundance was also discernible. Results of canonical correspondence analyses revealed that the progression of a diatom bloom, the emergence of dinoflagellates and the occurrence of intermittent blooms of the mixotrophic flagellate Eutreptiella marina were closely linked to factors such as higher temperature, salinity and phosphate concentration. Grazing by the herbivorous−bacterivorous ciliate communities may have controlled the blooms of undesirable groups of phytoplankton, ensuring better shrimp growth, higher survival and a lower food conversion ratio. Effective uptake of ammonium and nitrate by the blooming diatoms and phytoflagellates possibly prevented nutrient concentrations from reaching toxic levels, thereby generating an eco-friendly aquaculture water discharge into the adjacent ecosystem.