Rapidly growing economies often have high population growth, resulting in agricultural expansion in rural areas and increased water demand in urban areas. Conversion of forests and woodlands to agriculture may threaten safe and reliable water supply in cities. This study assesses the regulating functions and economic values of forests and woodlands in meeting the water needs of two major cities in Tanzania and proposes an integrated modelling approach with a scenario-based analysis to estimate costs of water supply avoided by forest conservation. We use the process-based hydrological Soil and Water Assessment Tool (SWAT) to simulate the role of woody habitats in the regulation of hydrological flow and sediment control. We find that the forests and woodlands play a significant role in regulating sediment load in rivers and reducing peak flows, with implications for the water supply from the Ruvu River to Dar es Salaam and Morogoro. A cost-based value assessment under water treatment works conditions up to 2016 suggests that water supply failure due to deforestation would cost Dar es Salaam USD 4.6-17.6 million per year and Morogoro USD 308 thousand per year. Stronger enforcement of forest and woodland protection in Tanzania must balance water policy objectives and food security.