Nutrient supply is a key bottom-up control of phytoplankton primary production in lake ecosystems. Top-down control via grazing pressure by zooplankton also constrains primary production and primary production may simultaneously affect zooplankton. Few studies have addressed these bidirectional interactions. We used convergent cross-mapping (CCM), a numerical test of causal associations, to quantify the presence and direction of the causal relationships among environmental variables (light availability, surface water temperature, NO3 -N, and PO4 -P), phytoplankton community composition, primary production, and the abundances of five functional zooplankton groups (large cladocerans, small cladocerans, rotifers, calanoids, and cyclopoids) in Lake Kasumigaura, a shallow, hypereutrophic lake in Japan. CCM suggested that primary production was causally influenced by NO3 -N and phytoplankton community composition; there was no detectable evidence of a causal effect of zooplankton on primary production. Our results also suggest that rotifers and cyclopoids were forced by primary production, and cyclopoids were further influenced by rotifers. However, our CCM suggested that primary production was weakly influenced by rotifers (i.e., bidirectional interaction). These findings may suggest complex linkages between nutrients, primary production, and rotifers and cyclopoids, a pattern that has not been previously detected or has been neglected. We used linear regression analysis to examine the relationships between the zooplankton community and pond smelt (Hypomesus nipponensis), the most abundant planktivore and the most important commercial fish species in Lake Kasumigaura. The relative abundance of pond smelt was significantly and positively correlated with the abundances of rotifers and cyclopoids, which were causally influenced by primary production. This finding suggests that bottom-up linkages between nutrient, primary production, and zooplankton abundance might be a key mechanism supporting high planktivore abundance in eutrophic lakes. Because increases in primary production and cyanobacteria blooms are likely to occur simultaneously in hypereutrophic lakes, our study highlights the need for ecosystem management to resolve the conflict between good water quality and high fishery production.