This research aimed at finding alternative options for conjunctive use of treated wastewater (TW) with groundwater (GW) minimizing the irrigation water from aquifers in the Al-Batinah region with the assistance of a Decision Support System (DSS). Oman is facing a three-facet problem of lowering of GW table, wastewater over-production and excess TW. Approved guidelines for use of TW with tertiary treatments are of two classes: class-A (for vegetables consumed raw), class-B (after cooking). The developed DSS is comprised of four management subsystems: (1) data management in Excel, (2) model and knowledge management by macro programming in Excel, (3) with linear programming (LP) optimization models including transportation algorithms, and (4) user interface with Excel or Visual Basic (VB). The results are based on two extreme scenarios: zero TW excess, and zero GW used for irrigation. The DSS could predict water balance for number of crop rotations, and based on adjustable cost variables farmer profit margins could be created. Crop selections and rotation could be done using LP optimizations while transportation algorithm could organize best locations and capacities for treatment plants and the wastewater collection and transportation to farming areas via treatment plants. The developed DSS will be very useful as a water management, optimization and planning tool.