Proper forest management focusing on water resources is crucial for supplying good-quality freshwater and protecting water sources. However, forests are declining due to urbanization, income generation, and agriculture triggering a potential worry for the sustainability of the water sources. The current study assesses the sensitivity of the water resources in Morogoro, Tanzania through historical forest cover losses. The river discharge and water quality trends are used to complement the assessment and discussions. Forest cover losses are analyzed based on the Sustainable Development Goals’ scale for permanent deforestation. The forest cover loss is increasing linearly and consistently to the discharge trends. Fecal contamination suggests the existence of human settlements in the catchments and that the forests are being invaded. The increasing levels of turbidity indicate that stormwater flows through bare soils carrying foreign materials toward the water sources. The findings create awareness amongst water resources stakeholders regarding the impacts of forest loss on the water supply systems in Morogoro and contribute to an approach for water resources sensitivity assessment that would be applied in other water supply systems.