A distributed hydro-environmental model is developed that achieves detailed analysis of the movement of water at a field-plot-scale resolution in a mesoscale watershed including lowland areas where, especially for agricultures, it is an essential need to get rid of redundant groundwater by drainage facilities such as rivers, canals and/or underdrains. For this, the problem geometry is meshed with unstructured cells of triangular shape. Profile of a column cell is zoned into two: surface zone and groundwater zone in which water movement is represented by combined tank and soil moisture sub-models, and well-defined two-dimensional unconfined shallow groundwater flow sub-model, respectively. The top-two sub-models serve to evaluate evapotranspiration, infiltration, soil water content, lateral surface water flow, and vertical percolation. The vertical percolation so evaluated is given as longitudinal recharge to the bottom sub-model for computing groundwater flow. Surface water–groundwater interactions through beds and stream-banks of perennial and ephemeral canals are considered by treating the canal courses as internal boundaries in the groundwater flow model. The finite volume method (FVM) that allows of unstructured mesh and produces conservative solutions is employed for groundwater flow computation. The model developed is applied to an actual watershed which includes a low-lying paddy area to quantify the hydrological impact of land-use management practices over a period of 29 years in which the farmland consolidation project was implemented and part of the paddy fields were converted to upland crop fields and housing lands. From the results obtained, it is concluded that the model presently developed lends itself to water—as well as land-use management practices.