The golden mussel (Limnoperna fortunei) is an invasive bivalve that has established itself in several South American river systems, impacting ecosystem functioning. Reservoir cascades provide their larvae with the means of rapid dispersal, but the relationship between environmental variables and larval stage structure remains unclear. In this study, the density of three L. fortunei larval stages and quantitative detection using DNA are analyzed in a cascade of five reservoirs in the upper Uruguay River Basin and associated with spatiotemporal variation in environmental parameters. The analysis of L. fortunei eDNA presence and absence in freshwater systems appears to be a valuable mapping tool; however, no significant link was found between the eDNA magnitude and the overall larval density. The increase in larval density was related to the fluctuation of environmental parameters over a year, with the highest average larval densities observed in the CN and ITA reservoirs, though no significant difference was observed between the five reservoirs, where D-shaped larvae predominated. During winter, larval density decreased significantly, however, other variables also contribute to species activity and development in the upper Uruguay River Basin reservoirs and may be considered limiting factors. The relationships between environmental parameters were evaluated using a multivariate model. The interaction between reservoir area and precipitation, water temperature, electrical conductivity, and dissolved oxygen had a significant effect on larval density but showed specific influences on each larval stage. Any increase in density was regulated by dissolved oxygen and electrical conductivity content at all larval stages. Furthermore, total phosphorus affected the density of F1 and F3 larvae. The interaction between reservoir area and precipitation, nitrate content, phosphate concentrations, and water temperature had the most influence on the density of F2 and F3 larval stages; the F1 stage was mainly affected by calcium concentrations. The isolated effect of precipitation also contributed to the density of F2 and F3 larvae. Our findings shed light on the interaction between different phases of golden mussel larvae and the main nutrients found in reservoirs, which may be a determining factor in the rise in density of the non-native species in these systems.