Megacities are facing serious water pollution problems due to urbanization, rapid population growth and economic development. Water is an essential resource for human activities and socio-economic development and water quality in urban settings has important implications for human and environmental health. Urbanization and lack of sewerage has left the water in Jakarta, Indonesia in a heavily polluted condition. Rigorous assessment of urban water quality is necessary to understand the factors controlling water quality conditions. We use trend analysis to assess the current water quality conditions in Jakarta, focusing on Biochemical Oxygen Demand (BOD), Dissolved Oxygen (DO), and Total Suspended Solids (TSS). In most monitoring stations analyzed, BOD and TSS concentrations have decreased over time, but from large starting concentrations. DO in most monitoring stations has increased. Although Jakarta’s water quality has shown some improvement, it remains heavily impaired. The average value of BOD is low in upper stream stations compared to middle and lower stream stations. BOD and TSS trends of some water quality stations in middle and lower streams show increasing trends. Cluster analysis results suggest three groups for BOD and TSS, and four groups for DO. Understanding water quality conditions and factors that control water quality suggest strategies for improving water quality given current trends in climate, population growth and urban development. Results from this study suggest research directions and management strategies to address water quality challenges.