The present study aimed to investigate the morphometric characters of fish species, Labeo rohita, Rita rita, Wallago attu and Mystus aor sampled from two aquatic habitats, Gomti River nearby Lucknow and Ganga River at Ghazipur, Uttar Pradesh, India. Both rivers are extremely cherished rivers as they are full of natural resources and highly rich in faunal and floral diversity. A total of 100 specimens of each fish species were collected during October, 2021 to January, 2022. The seventeen morphometric parameters were selected for the comparative differential analysis of population stocks of each fish species in two aquatic habitats. The quantitative measurements of all the morphometric characters delivered the important information about the growth of body parts of fishes in different aquatic ecosystem. The variations in morphometry of individuals of a species illustrated the alterations in the population status under the differential environmental circumstances. The approach of morphometric analysis can be a strategic tool to explore the body shape formation of fish species in different ecosystems. The analyzed data of morphometric dimensions of four fish species would be beneficial for the policy makers or planners to develop the scientific strategies for their protection and conservation. The findings will also set the scientific principles for the management and sustainable development of the commercially essential freshwater food fishes.