It is concerned that Egeria densa, a nonnative aquatic weed, could negatively affect Plecoglossus altivelis altivelis, a native fish species, in Japanese rivers. In this study, we examined the effects of E. densa and other environmental factors on P. a. altivelis in the Gonokawa River in Japan in August 2019, using environmental DNA (eDNA) method, unmanned aerial vehicle, and statistical modeling (simple linear regression and generalized linear model). The results of the simple linear regression indicated that the eDNA concentrations of P. a. altivelis were not significantly related to E. densa cover degree, but negatively related to water temperature in the study sites in the summer high-water temperature condition. The best model of the generalized linear model also indicated that water temperature had the highest correlation with the eDNA concentrations of P. a. altivelis. These results suggest that water temperature could influence the abundance of P. a. altivelis more than E. densa in the high-water temperature condition.