Climate change significantly affects aquatic ecosystems, driving morphological and physiological adaptations in estuarine fish. This study examined the impact of salinity, temperature, and dissolved oxygen variations on the morphological traits of Pseudotolithus elongatus in the Cross River Estuary, Nigeria. Over a 12-month period, a total of 240 fish samples were collected across three salinity zones (low: <10ppt, medium: 10–20ppt, high: >20ppt). Key environmental parameters were recorded alongside morphological measurements, including body depth, caudal fin length, and total length. Data analysis involved ANOVA, Pearson correlation, principal component analysis (PCA), and multiple linear regression. Significant morphological differences were observed among salinity zones, with deeper bodies and larger caudal fins in higher salinity zones, reflecting adaptations to stronger tidal currents and elevated salinity. Temperature positively correlated with body depth (R² = 0.87, P< 0.001), highlighting thermal stress as a driver of morphological shifts. The analysis of the principal components identified body depth and caudal fin length as the main contributors to morphological variation, explaining 47.2% of the variance. Regression analysis revealed salinity and temperature as significant predictors of body depth (Adjusted R² = 0.72, P< 0.001), while dissolved oxygen showed a modest negative effect. These findings underline the plasticity of P. elongatus in response to climate-induced environmental changes, with implications for fisheries management under shifting ecological conditions. Adaptive strategies incorporating environmental monitoring and sustainable resource management are recommended to mitigate climate change impacts on fish populations.