Invasion, spread and predominance of alien invasive fishes were studied in 950-km-long stretch of the Yamuna River. The fish yield ranged between 32 t/km/yr to 240 t/km/yr and the catch of alien invasive fishes dominated over local fishes in the fishery, which was over 96% at Etawah. The calculated Invasion Coefficient Index (I_xi) of alien invasive fishes was in the range of 0.12 to 0.31 indicating a major loss to the local fish diversity. The calculated Pearson’s correlation coefficient was found to have positive correlation of 0.757 and 0.710 for common carp and tilapia respectively with locally captured Indian major carps (IMC). The results of this study highlighted how unintentional spread of alien invasive fishes due to rapid aquaculture diversification and intensification has invaded into the Yamuna River causing severe loss to the local fishery. The invasion of alien fishes has been mapped for the Yamuna River at different locations using GIS tools. The results of this study invite attention on the management and sustainability of the local fishery and ecosystem health of the river.