This paper investigates land-use as the cornerstone of spatial planning in rapidly urbanising contexts, focusing on the critical gaps at the mesoscale between centralised vision and local implementation. By exploring Java’s complex desakota landscapes, this study employs an innovative GIS-based land-use cluster analysis using multidimensional parameters—including slope, population density, agricultural land, forest cover, and surface water—to categorise land-use patterns. The resulting mesoscale clusters reveal cohesive functional territories that transcend traditional political boundaries, articulating distinctive ‘mixtures’ of urbanity within Java’s rural-urban continuum. This approach not only captures socio-environmental dynamics across administrative silos but also establishes a new strategic framework for regional planning challenges. By advancing boundary-making beyond mere political convention to reflect on-the-ground ecological and functional coherence, this framework responds to the urgent global challenge of reconciling accelerating suburban and regional development pressures with the preservation of local communities, agricultural systems, and natural landscapes.