This study assessed flood inundation of the Ciliwung River Basin, Greater Jakarta to improve the urban water environment under climate change and unplanned urbanisation. The 1-day maximum precipitation data for 50- and 100-year return period under current and future climate conditions were used to assess the impact of climate change. Precipitation output of the MRI-CGCM3, MIROC5, and HadGEM2-ES General Circulation Models (GCMs) with RCP 4.5 and 8.5 emission scenario over periods 1985–2004 and 2020–2039 representing current and future climate conditions, respectively, were used. Similarly, land use data of 2009 and 2030 were used to represent the current and future conditions, respectively. The HEC-HMS model was used to simulate the river discharge at Katulampa, which represents the outlet location for the hydrologic modelling and the inlet location for the flood inundation modelling. FLO-2D, a two-dimensional hydrodynamic model, was used to simulate current and future flood inundation simulations. Increasing flood inundation areas and depths (6% to 31% for different GCMs) in the future reveal the need to improve flood management tools for the sustainable development of urban water environments.