Hydraulic conductivity sometimes exhibits complicated spatial variation over a site. A thorough understanding of the spatial distributions of hydraulic conductivity helps to make deterministic models of groundwater more accurate. This study presents a novel procedure that combines simulated annealing algorithms (SA) and the shortest distance method (SD) with the modular three-dimensional groundwater flow model (MODFLOW). The procedure is applied to a hypothetical site with groundwater-monitoring wells to minimize the difference between simulated and observed hydraulic head for optimal zoning of the spatial distribution of hydraulic conductivity. The results of this optimal zoning method indicate that this new procedure not only improves the efficiency of optimization, but also increases the probability of finding the global optimum, minimizing the errors of the hydraulic head simulated by MODFLOW in two scenarios, one with known and the other with unknown hydraulic conductivity. The results also illustrated that the procedure can effectively determine and delineate hydrogeological zones.