This study is part of a large-scale project aimed at rehabilitation of the Israeli Coastal Aquifer. Development of a regional 3-D, transient flow and transport model of the hydrological system in the vicinity of the Dan Region Sewage Reclamation Project (SHAFDAN) is presented. The SHAFDAN facilities include five infiltration ponds to which high-quality treated effluent is sent for soil aquifer treatment (SAT). The ponds are surrounded by recovery wells that abstract the treated water and prevent it from spread to fresh water pumping zones. The model is used for estimating the spread of SHAFDAN water and testing operational scenarios. A 30-year forecast run showed that significant spread in the aquifer from the southern ponds is expected. The model examined two possible solutions for reducing spread: (1) increased pumpage in existing recovery wells; (2) additional wells on the eastern side of the ponds. The results show that the first solution reduced spread more effectively, but also led to rapid seawater intrusion from the west. The study demonstrates how changes in pumping regime affect spread. The model is, therefore, an appropriate tool for evaluating SHAFDAN operation in addition to its role in planning rehabilitation of the aquifer as a whole.