Emerging evidence suggests that zooplankton production is affected by physiological and nutritional constraints due to climate change and eutrophication, which in turn could have broad implications for food-web dynamics and fisheries production. In this study, we developed a resource-based zooplankton production dynamics model that causally links freshwater cladoceran and copepod daily production-to-biomass (P/B) ratios with water temperature, phytoplankton biomass and community composition, and zooplankton feeding selectivity. This model was used to evaluate constraints on zooplankton growth under four hypothetical scenarios: involving natural plankton community seasonal succession; lake fertilization to enhance fisheries production; eutrophication; and climatic warming. Our novel modeling approach predicts zooplankton production is strongly dependent on seasonal variation in resource availability and quality, which results in more complex zooplankton dynamics than predicted by simpler temperature dependent models. For mesotrophic and hypereutrophic lakes, our study suggests that the ultimate control over zooplankton P/B ratios shifts from physiological control during colder periods to strong resource control during warmer periods. Our resource-based model provided important insights into the nature of biophysical control of zooplankton under a changing climate that has crucial implications for food web energy transfer and fisheries production.