Managing eutrophied systems using only nutrient decreases to impose bottom–up control can be economically and ecologically challenging. Top–down controls through increased consumption have sometimes effectively controlled phytoplankton blooms. However, mechanistic insights, especially on possible trophic cascades, are less understood in brackish, species‐poor coastal waters, where large cladocera are absent. In this study, we set‐up large mesocosms for three consecutive years during the growing season. One set of mesocosms contained mesopredators (gobies and shrimps), whereas the other mesocosms had no such mesopredator present. The results were standardized to monitoring data from the ecosystem to track possible differences between treatments and the system. We found that mesopredator mesocosms showed lower turbidity, phytoplankton biomass and nutrients compared to no‐mesopredator mesocosms, and compared to the ecosystem. This decrease allowed macrophytes to colonize water depths only sparsely colonized in the ecosystem. Rotifer biomass increased in mesopredator mesocosms compared to the ecosystem and to the no‐mesopredator mesocosms. Likewise, copepod biomass that potentially grazes upon rotifers and other microzooplankton decreased in mesopredator mesocosms. No‐mesopredator mesocosms were colonized by an omnivorous mesograzer Gammarus tigrinus, potentially creating additional pressure on macrophytes and increasing grazing‐mediated nutrient release. Zooplankton was not able to control the non‐nutrient limited phytoplankton. We propose a new mechanism, where a higher mesopredator density will increase grazing on phytoplankton by promoting microzooplankton capable of grazing on picophytoplankton. This proposed mechanism would contrast with freshwater systems, where a decrease of zooplanktivorous fish would promote larger phytoplankton grazer like cladocera. Biomanipulation in such species‐poor eutrophic coastal waters may be more successful, due to less trophic pathways, that can cause complex top–down controls like in other systems. Stocking eutrophic coastal waters with gobies and shrimps may be an alternative biomanipulative approach rather than selectively removing large piscivorous or omnivorous fish from eutrophic coastal waters.