Environmental conditions of water bodies vary because of natural (climate change) or anthropogenic factors, such as damming, urbanization, pollution, etc., which determine the health of the ecosystem and its fishery potential. Phenotypic and biological traits (fecundity, growth, feeding habits, etc.) of fish populations vary in response to diverse environmental conditions of their habitats. Therefore, a total of 150 adult matured female individuals of Trichogaster bejeus were selected from all captured (279) individuals from river Ganga and its tributaries (Gomti and Yamuna) of Gangetic plain to study the microelements and the shape of sagittal otolith along with some morphological and biological trait variations. The microchemistry (element/Ca) of otolith was evaluated using inductively coupled plasma-optical emission spectroscopy. Uni- and multivariate statistics were used for analysis of the data. The element ratios, such as Cu/Ca, Cr/Ca, Pb/Ca, Sr/Ca, Zn/Ca, Ni/Ca, Ba/Ca, Mn/Ca, Mg/Ca, and Fe/Ca, were analyzed using linear discriminant function analysis which showed re-classification accuracy of 94% in the otoliths of different populations of the fish. Analysis of geometric morphometric and shape indices (roundness, rectangularity, ellipticity and aspect ratio) indicated re-classification success of 80.3% and 67.3% respectively. Leave-one-out classification of the combined data of two techniques (shape analysis and chemistry) based on otolith reallocates the individuals to their respective populations with an overall accuracy of 96.6%. Otolith shape, chemistry, and biological traits discriminated the sub-population of T. bejeus which is effective for sustainable management to maintain lifelong sustainability in natural environments.