The outcome of a conventional planning process is often a spatial plan which integrates the physical and fiscal development proposals prepared based on an administrative boundary that is entirely arbitrary. Due to its obvious demerits, this study therefore attempts to establish the significance of the ecological boundary-based planning approach which could address most of the environmental problems of consideration. Accordingly, the Kuttanad Wetland System in Kerala, India, is taken a case study for detailed analysis and exploration of the concept. The study demonstrates the correlation between the elevation profile of the area and the flood water pattern and signified how elevation profile impacts the accumulation of floodwaters. It was followed by the land use land cover (LULC) change analyses under five scenarios during 2005, 2011, 2015, 2025 (projected), and a regulated condition (idealistic case). The hydrologic modeling using SWAT and HEC-RAS substantiated that the increasing built-up and wasteland with the reduction in vegetation would accelerate the surface runoff rate.1The projected LULC map of 2025 signified that the intensity of floods increased when the percentage built-up and wasteland increased. Similarly, the sprawl when curbed along with upland afforestation and floodplain restoration, lowered the intensity of floods. The study concludes by putting planning recommendations and policies showcasing the significance of ‘eco-urban and regional planning’, as a new concept and a framework that must be pursued at the earliest.