East African forested mountain regions are vital in generating and supplying water resources to adjacent arid and semi-arid lowlands. However, these ecosystems are under pressure from both climate and land use changes. This study aimed to analyze the effects of climate and land use changes on water yield using the Budyko framework as a first-order conceptual framework assuming steady-state for pristine/protected forested areas. For nine selected forested water towers in East Africa, the amount and distribution of water resources and their decadal changes were analyzed. Results show that most areas inside and outside the water towers are under pressure from human influences. Water yield was more sensitive to climate changes compared to land use changes within the selected East African water towers themselves. However, for the surrounding lowlands, the effects of land use changes had greater impacts on water yield. We conclude that the East African water towers have seen a strong shift towards wetter conditions, especially in the period of 2011–2019, while, at the same time, the potential evapotranspiration is gradually increasing. Given that most of the water towers were identified as non-resilient to these changes, future water yield is likely to also experience more extreme variations.