Environmental concerns have necessitated the development of computational models predicting pollutant dispersion in natural water systems. Due to the ill-posed nature of the inverse contaminant transport equation, solving this equation using all stable and convergent inverse methods is impossible. Factors such as river geometry, unsteady and non-uniform flow, and tidal influences add to the complexity of the inverse problem. These factors have prompted the evaluation of Group Preserving Scheme for environmental applications. The inverse solution method derives a general equation for solving ordinary differential equations by addressing a dynamical system at negative time steps, ensuring convergence. Three test cases have been presented to evaluate Backward Group Preserving Scheme (BGPS). These have included validation using observational data from Missouri River, inverse simulation in a tidal river, and sensitivity analysis of parameters such as pollutant patterns, advection, dispersion, and decay coefficients. The dataset includes calibrated data from Missouri River, which demonstrated high accuracy, with Mean Relative Error (MRE) ranging from 2.8% to 5.0% for the inverse model. Under tidal conditions, accuracy decreases over time but remains robust, with a Nash–Sutcliffe efficiency of 0.77–0.96 and an MRE of 0.9%–5.9%. Sensitivity analysis revealed optimal model performance for Péclet numbers greater than 500. The model performed best with gradual, wide-peaked pollutant patterns and moderate decay rates (Damköhler number between 5 and 10). BGPS proves effective for transport simulation and concentration history reconstruction in complex rivers, including those with tidal influences, offering a robust tool for water contamination analysis in various flow conditions.