Despite the ecological and economic importance of Acacia senegal, little is known about the effects of anthropogenic disturbances on its natural regeneration patterns and population structure. We investigated the effects of these factors within the Lake Baringo woodland ecosystem. Data was collected from 60 plots of 20 m × 20 m systematically distributed in four A. senegal-dominated populations within the Lake Baringo woodland. Sample populations spanned a degradation gradient measured by a population disturbance index (PDI). Trees were measured for diameter at breast height (DBH) and categorized by growth stages: seedling, sapling and adult tree. Higher seedling and sapling densities were recorded in lightly than heavily disturbed populations, but only sapling density was significantly different between the two disturbance levels (P = 0.02). Lightly disturbed populations revealed a reversed J-shape size-class distribution (SCD) indicative of stable structure unlike the heavily disturbed populations. The quotient and permutation indices indicated unstable populations with episodic recruitment and mortality. Our study reveals that natural regeneration and population structure of A. senegal were affected majorly by selective harvesting and heavy browsing. Suitable management strategies to control livestock grazing and illegal tree harvesting within the woodland is required to promote conservation of the species genetic resources