Acacia encompasses a keystone genus across the Middle Eastern and African drylands. This study assesses the dynamics of Acacia populations in two ephemeral stream channels (Nahal Naomi and Nahal Yael) in the hyper-arid Arava region following the establishment of a dam in the upstream channel of Nahal Yael and a long-term regional drought episode. The assessments were conducted at the individual and population levels, for a period of 45 years (during 1972, 1994 and 2017). In Nahal Naomi, the population increased by 35% during 1972–1994 (a relatively rainy period) and experienced low mortality (net change of +1.6% year−1). However, following a regional drought episode between 1995 and 2009, this population decreased by 57% (net change of −2.5% year−1). In Nahal Yael, the acacia population declined by 66% during 1972–1994 (net change of −1.6% year−1). Between 1994–2017, this population was co-affected by dam and drought, with no recruitment, and declined by 70% (net change of −2.0% year−1). By examining the tree’s specific location, species, age and state of preservation of dead individuals, we identified factors that influence tree mortality, and highlighted the adverse impacts of natural and anthropogenic disturbances on Acacia populations in hyper-arid environments.