In response to escalating worldwide groundwater dependence amid climate change, accurate estimation of sustainable groundwater yield becomes crucial. This study investigated the impact of groundwater abstraction on tree mortality in Namibia. We compared tree mortality around production boreholes with monitoring boreholes and we correlated groundwater decline rates with tree mortality, establishing a model from which we derived a groundwater decline rate range limit. Ana tree mortality was significantly higher (P = 0.01) around production boreholes (13.3%) than around monitoring boreholes (0%). In the dammed Swakop River, Ana tree mortality correlated with decline rates (rS = 0.64, P < 0.01). The study suggests that decline rates of above 0.2–0.23 cm day−1 may cause elevated mortality (3–7%) and should not be sustained for extended periods. Rates exceeding 0.5 cm day−1 should be avoided, while monitoring is recommended for rates between 0.23 and 0.5 cm day−1. Woodlands in rivers with altered flood frequencies may be more sensitive to groundwater abstraction than previously thought. The study's methods offer a universal framework for refining sustainable yield calculations worldwide.