The disposal of the excessive volume of degraded water coming from agricultural drainage systems is a serious environmental and economic issue, since a significant load of agrochemicals and salts contaminates water bodies downstream. An integrated on-farm drainage management (IFDM) system is an effective method of treatment by successively irrigating zones with drainage water. Each zone is cultivated with crops that have increasing tolerance to salinity, so that the drainage water effluents are minimized to an extent that the final drainage water volume is collected into an evaporation pond. The methodology of the system is proposed herein for a regional irrigation-drainage network (E1 in Agoulinitsa irrigation district in western Greece) as a method of reducing the disposal of agrochemicals in the coastal environment. Based on the design principles of an IFDM system, both the surface area of every irrigation zone and the costs of installing and operating the system are assessed. A scenario regarding the volume of drainage water that must be treated is examined as a sensitivity analysis. The results show that almost 15% of the cultivated area must be bounded for non-productive uses, resulting in a significant economic impact on the net present value of the investment.