In an aquifer, heterogeneity plays an important role in governing groundwater flow. Hence, aquifer characterization should involve both the pattern and values of the hydrogeological parameters. A new analytical solution describing the one-dimensional groundwater flow in a multi-zone unconfined aquifer is presented, and a methodology developed from the analytical solution and a heuristic approach for determining the pattern and values of the aquifer parameters are proposed. The analytical solution demonstrates that the hydraulic head varies spatially and is influenced by aquifer heterogeneity. Simulated annealing, a heuristic approach, is incorporated with the solution to simultaneously identify the pattern and values of the hydraulic conductivity for a horizontal multi-zone unconfined aquifer. This approach may be used to give an approximate result for a two-dimensional problem by dividing the model area into a number of transects along the transverse direction, identifying the parameter values along the longitudinal direction for each transect, and then smoothing the identified results.