Climate change and land-use practices can enhance lake eutrophication and browning, which influence phytoplankton composition by decreasing the availability of food high in nutritional quality (algae) and increasing the abundance of low-quality food (terrestrial detritus, bacteria) for herbivorous zooplankton. Nutritionally valuable algae for zooplankton are rich in essential biomolecules such as amino acids, polyunsaturated fatty acids (PUFAs), sterols, and phosphorus. We performed laboratory experiments and showed a stronger positive relationship between zooplankton (Daphnia) cumulative offspring number and availability of high-quality algae (Cryptophytes: Rhodomonas/Cryptomonas; and Chrysophytes: Mallomonas) than with intermediate-quality (Chlorophytes: Acutodesmus) or poor-quality (Dinoflagellates: Peridinium) algae. The higher cumulative offspring number of Daphnia was a result of higher amounts of total ω-3 and ω-6 PUFA, proteins, sterols, and amino acids in the algal diets. The experiments also showed that even a small addition of high-quality algae (Rhodomonas) to intermediate-quality (Acutodesmus) or low-quality (bacteria, heterotrophic nanoflagellates, or terrestrial organic matter) diets can enhance the Daphnia cumulative offspring production. Our carbon mass balance calculation for a eutrophic clearwater lake and an oligotrophic polyhumic lake showed that the abundance of high-quality phytoplankton (cryptophytes, chrysophytes, diatoms) among total particulate organic carbon was minor (8.7% [SD 2.4%] and 6.5% [7.0%]). We modeled Daphnia diets (i.e., resource assimilation) using a fatty acid mixing model. Our analyses showed that Daphnia were able to locate high-quality algae (cryptophytes, chrysophytes, and diatoms) more effectively during cyanobacteria blooms in a eutrophic lake (55% [SD 12%]) than in a polyhumic lake (25% [10%]). Nevertheless, our results show that intense eutrophication and browning diminish assimilation of high quality algae, limiting Daphnia biomass production.