This study deals with the formulation of a coupled flow-mass transport inverse problem using the weighted least squares (WLS) estimation concept. The parameters of coupled flow-mass transport model are identified based on GNM, SA, and GA. The resulting parameter estimation entails inversion of spatial and temporal distribution of head and concentration. An FEM model is developed for computing the distribution of head and concentration in a confined aquifer. The inverse model based upon GNM, SA, and GA approaches identifies flow and transport parameters within each zone. Aquifer parameters estimated by GNM are compared with those obtained by SA and GA. Reliability of the estimated parameters is assessed using sensitivity and variance-covariance analysis. An optimum parameter structure is identified by computing and analyzing the sum of squared head and concentration residuals for different alternate model structure. GNM, SA, and GA inverse models are adequately modified for their application to the field problem.