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At present, application of GIS network analysis for agricultural drainage management is limited, although the nature of water flow within a drainage network is by and large in a similar way to that of, for example, the traffic flow over a road network. This is due to the limitation of the current GIS network model, which has difficulties in handling the complexity and event-based dynamic nature of the drainage network. This research therefore focuses on drainage management problems in a floodplain where drainage is controlled by the natural and artificial drainage networks. GIS network capabilities were employed, with enhancements of specific needs for the drainage simulation. A specialized three-dimensional network model was developed to allow computation of important parameters for network analysis, making dynamic simulation of drainage corresponding to individual rainfall events possible. Test simulation results indicate that the simulation tends to overestimate the discharge volume and pollutant, but the relative error level is low with an average of 7.3% and maximum of 12.7%.