Macrozooplankton may affect algal and microbial plankton directly through grazing or predation and indirectly through nutrient regeneration. They may also affect potential prey positively by removing alternative predators. Here, we examined the effects of a cladoceran (Daphnia) and a calanoid copepod (Eodiaptomus) on algal and microbial plankton in a Japanese lake using in situ experiments in which we manipulated the nutrient supply and biomass of these macrozooplankton. The response of algal and microbial plankton to macrozooplankton was diverse and varied depending on the level of nutrient supply. Eodiaptomus seemed to feed mainly on large algae (>20 µm) and microzooplankton, while direct grazing by Daphnia on algae, bacteria, heterotrophic nanoflagellates (HNF), and microzooplankton (ciliates, heliozoa, and rotifers) was pronounced. Trophic linkages within these microbial plankton was also suggested; bacteria were grazed by HNF and these in turn were grazed by microzooplankton. When the nutrient supply was high, both HNF and microzooplankton were exposed to higher amounts of algae and lower bacterial abundance. Moreover, nutrient regeneration by daphnids and Eodiaptomus copepods seemed to differentially stimulate the growth of algae and bacteria. The results suggest that the relationship between macrozooplankton and microbial plankton cannot be fully understood without taking into consideration not only the feeding characteristics of the macrozooplankton, but also the food web structure, the subsidized algal resource, and nutrient regeneration from the macrozooplankton.