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A multidisciplinary study with the main objective to develop an environmentally sound water management to be applied in peat land agriculture has been conducted. The output of this study is a water level controller, a computer software that incorporates two dimensional equation of water flow in saturated soil and fuzzy controller with taking into account the soil physical properties of peat soil under consideration and its hydrological conditions. By using this system the excessive water extraction or reduction, of which in many tropical peat soils will cause soil subsidence due to irreversible deformation, can be prevented. The system has been tested by conducting field experiments for some tropical peat lands in South Sumatra, Indonesia, to see the applicability of the system in maintaining the desired water levels. The actual water level was measured by means of pressure transducer while water inflow and outflow were undertaken by the use of electric pumps. A simulator, based on equations of soil water flow, tides, and control algorithm, was developed and used to intensify the research, minimize failure, and cost of field experiment or application. This simulator can also be used as a tool for obtaining appropriate size of specific peat land agriculture within the capability of water management. Hopefully, this system can be used as a valuable assistance in designing an agricultural plot converted from peat land and enables the determination of operation cost of water management in a field scale.