In Jakarta, climate change has been detected through rising air temperatures, increased intensity of rainfall in the wet season, and sea level rise. The coupling of such changes with local anthropogenic driven modifications in the environmental setting could contribute to an increased probability of flooding, due to increase in both extreme river discharge and sedimentation (as a result of erosion in the watersheds above Jakarta and as indicated by sediment yield in the downstream area). In order to respond to the observed and projected changes in river discharge and sediment yield, and their secondary impacts, adaptation strategies are required. A possible adaptation strategy is through policy making in the field of spatial planning. For example, in Indonesia, presidential regulation number 54 year 2008 (Peraturan Presiden Nomor 54 Tahun 2008—Perpres 54/2008) was issued as a reference for the implementation of water and soil conservation. This paper assesses the impact of climate and land cover change on river discharge and sediment yield, as well as the effects of Perpres 54/2008 on that river discharge and sediment yield. The spatial water balance model Spatial Tools for River Basins and Environmental and Analysis of Management Option was used for the runoff computations, whilst the Spatial Decision Assistance of Watershed Sedimentation model was used to simulate erosion, Sediment Delivery Ratio, and sediment yield. The computation period is from January 1901 to December 2005, at the scale of the following watersheds: Ciujung, Cisadane, Ciliwung, and Citarum. During the twentieth century, computed average discharge in the downstream area (near Jakarta) increased between 2.5 and 35 m<Superscript>3</Superscript>/s/month, and sediment yield increased between 1 × 10<Superscript>3</Superscript> and 42 × 10<Superscript>3</Superscript> tons/year. These changes were caused by changes in both land cover and climate, with the former playing a stronger role. Based on a computation under a theoretical full implementation of the spatial plan proposed by Perpres 54/2008, river discharge would decrease by up to 5 % in the Ciliwung watershed and 26 % in the Cisadane watershed. The implementation of Perpres 54/2008 could also decrease the sediment yield, by up to 61 and 22 % in the Ciliwung and Cisadane watersheds, respectively. These findings show that the implementation of the spatial plan of Perpres 54/2008 could significantly improve watershed response to runoff and erosion. This study may serve as a tool for assessing the reduction in climate change impacts and evaluating the role of spatial planning for adaptation strategies. Copyright Springer Science+Business Media Dordrecht 2014