Land-use changes from forest to other use will affect watershed hydrological system that lead to water availability in Leitimur Peninsula watershed, Ambon Island. It aims to analyze sustainability index and sensitive attribute of watershed management and to design watershed management model in supporting sustainability of water resources in Leitimur Peninsula. The analysis applies the Multidimensional Scaling (MDS) model and the dynamic model (Stella). The findings signifies that multidimensional sustainability status is 50.97% indicating quite sustainable, while the best management model is by performing land and forest rehabilitation (LFR) and agricultural extensification through agro-forestry system.