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Submerged macrophytes promote water clarity in shallow lakes in temperate regions via zooplankton refuge, allelopathy, and nutrient competition with phytoplankton, thereby increasing zooplankton grazing. However, in high-altitude Andean ecosystems, these interactions in shallow lakes have received far less attention. To understand the role of submerged plants in a relatively cold ecosystem (typical for the Andean region), two 100 L experiments were conducted in Yahuarcocha Lake, which has a permanent cyanobacterial bloom. In our first experiment, we evaluated the response of the cyanobacteria bloom to different concentrations of <i>Egeria densa</i> (15%, 35%, and 45% PVI). In the second experiment, we investigated the interactions between <i>E. densa</i> (35% PVI), zooplankton, and the small-sized fish <i>Poecilia reticulata</i> as well as their impacts on phytoplankton. We found a strong reduction in cyanobacteria in the presence of <i>E. densa</i>, whereas <i>P. reticulata</i> promoted cyanobacteria dominance and zooplankton had a null effect on phytoplankton. Remarkably, the combination of <i>E. densa</i>, fish, and zooplankton substantially reduced the algae. Our findings showed that the cyanobacteria bloom decreased in the presence of <i>E. densa</i>, thereby increasing the water clarity in the high-elevation eutrophic ecosystem in the Andes. This effect depended on the plant volume inhabited and the small-sized fish biomass.