Mapping mountain ecosystems is needed for local planning. Ecosystem boundaries are influenced by interrelated physical and environmental factors rather than singular physical features. Tropical mountain landscapes exhibit diverse surface patterns, impacting their terrestrial ecological systems. Using river network data and Digital Terrain Models (DTMs), we delineated ecosystem groups based on seven surface parameters: river order, channel sinuosity, elevation, slope, aspect, roughness index, and curvature. A multivariate clustering method identified ecosystem groups with similar attributes, further clarified using geological and land cover maps to account for surface and subsurface material variations and their processes. Our analysis identified five distinct ecosystem units: the young Sumbing volcanic peak, old Sumbing volcanic peak, old Sumbing volcanic slope, transitional volcanic, and old Menoreh volcanic ecosystems. The parameters that have a strong influence in limiting these units are elevation, slope, curvature, and roughness. Despite being part of the same mountain range, these ecosystems exhibit markedly different physical land characteristics. The surface-boundary-based delineation method offers a straightforward approach to spatially defining mountain ecosystems. This method enhances spatial planning by aligning with land capacity and ecosystem service provisioning. The derived spatial boundaries represent not only the current natural capital but also dynamic limiting factors. This approach demonstrates the potential for detailed, effective landscape management in complex mountainous regions.