Ciliwung Watershed is the most developed area in Indonesia. However, development needs have caused overexploitation of the available resources, which have eventually caused deterioration of the environment of this watershed, and caused several areas to be more prone to natural hazards. This study develops certain Geographic Information System models to identify the physical-environmental characteristics of the watershed, in an attempt to avoid further improper resources utilization. These models yield the soil erosion critical areas, landslide potential areas, the spread of sea water intrusion, land subsidence potential areas, surface runoff characteristic, natural hazards prone areas, and groundwater recharge area.Based on these yielded characteristics, the general physical capability of this watershed can be delineated, which consists of five capability zones : Zone I, the flood prone area that also occupies by seawater intrusion and potential land subsidence areas; Zone II, the area that is affected by excessive groundwater withdrawal, which has sea water intrusion areas and prone to land subsidence; Zone III, the groundwater recharge area for Jakarta Plain; Zone IV, the most capable area for physical development; and Zone V, upper part of the watershed which has landslide potential areas, soil erosion critical areas, and volcanic eruption prone areas.