Submerged macrophytes play crucial roles in maintaining the stability of clear-water states in shallow lakes. Recent stable isotope studies have shown that crustacean zooplankton can utilize submerged macrophyte carbon, but macrophytes alone cannot support the growth and reproduction of such grazers, being deficient in highly unsaturated fatty acids (HUFA). We hypothesized that flagellates feeding on macrophytes can synthesize HUFA and thereby support crustacean zooplankton. To test this hypothesis, we conducted a feeding experiment in which Daphnia magna were provided with a diet of submerged macrophyte Hydrilla verticillata detritus which had been degraded by lake microbes. The chlorophyte Scenedesmus bijuga and undegraded macrophyte detritus were used as controls for comparison of Daphnia's performance. Using biochemical analysis, we examined how the degradation process affected the food quality of the macrophyte. Flagellates were subsequently isolated from the degraded macrophyte and cultured heterotrophically to detect their HUFA synthesis. The 5-day degraded H. verticillata showed significantly higher HUFA concentrations than undegraded macrophyte detritus. They supported better Daphnia performance than undegraded macrophyte, being comparable with S. bijuga. Two isolated flagellates (SL-1 and SL-2), identified as Ochromonas sp. and Poterioochromonas sp., were found to contain HUFA when cultured heterotrophically without dietary sources of fatty acids, suggesting their HUFA synthesis ability. Our results demonstrate that submerged macrophytes may thus indirectly support crustacean zooplankton via flagellate mediation. As crustacean zooplanktons are of key importance for water quality in the grazer control of phytoplankton, this microbial facilitation may contribute to the maintenance of macrophyte clear-water conditions in shallow lakes.