This review features recent updates on planktonic community alteration attributed to shellfish farming across three major drivers: predation, nutrient availability and the hydrodynamic environment. The grazing pressure generated by filter‐feeder communities (shellfish and epibionts) constitutes a ‘top‐down’ control of planktonic communities in aquaculture areas, inducing a significant depletion of planktonic organism concentration. By selecting larger cells during the filtration process, shellfish also favour smaller organisms in the water column, leading to the dominance of the latter. Direct excretion and the benthic alteration process tend to fertilise the water column and significantly stimulate primary production. The associated epibiont community particularly contributes to this regeneration process. The expected consequence of increasing nutrient availability is generally a planktonic shift in favour of small planktonic species. However, investigation on the relationship between planktonic structure and nutrient conditions has revealed a wide complexity and variability. Finally, all structures used in shellfish farming activities interact with water currents and tend to significantly increase the residence time of planktonic organisms inside shellfish farming areas. In grazing‐dominated systems, an increase in residence time tends to increase the exposure time of planktonic populations to detrimental conditions, reducing biomass and production. The general consequences of shellfish farming are a decrease in primary production in farming ecosystems, and a possible alteration of structure and functioning of planktonic communities. The implications of shellfish farming also appear to be quite different from other aquaculture activities such as fish farming, which tend to promote primary production leading to eutrophication process.