Mesozooplankton are key components in the marine environment, linking the microbial food web and the classic food chain. Yet uncertainties remain on how mesozooplankton mediate the dynamics of prey communities through their complex feeding patterns. To examine mesozooplankton-mediated trophic interactions, we performed shipboard incubations using food removal and dilution methods during 4 cruises in the Pearl River estuary (PRE), Southern China. Our results revealed that mesozooplankton had diverse effects on different size fractions and taxonomic groups of phytoplankton via a combination of strong feeding selectivity and trophic cascades. High ingestion rates by mesozooplankton suppressed the accumulation of microphytoplankton (>20 µm), whereas low ingestion rates by mesozooplankton and resultant trophic cascades promoted the biomass of nano-sized (2-20 µm) and pico-sized (0.7-2 µm) phytoplankton. Among phytoplankton groups, diatoms were passively selected by mesozooplankton despite their high concentrations in natural seawater, whereas dinoflagellates and cryptophytes were actively preferred by mesozooplankton in spring and autumn. Similarly, ciliates were also preferred by mesozooplankton despite their lower biomass compared to phytoplankton, which induced a trophic cascade that indirectly increased the biomass of smaller phytoplankton. The overall feeding effect of mesozooplankton on phytoplankton was determined by the balance between direct grazing rates and indirect compensation with trophic cascades. The degrees of carnivory of the mesozooplankton, which determined the strength of trophic cascades, varied among seasons, resulting in weak control of algal blooms by mesozooplankton. Our findings provide insights into the complex trophic interactions between mesozooplankton and other plankton groups in dynamic natural ecosystems.