Tropical forests can vary enormously in their 3D structure and dynamics even within the same landscape. However, the drivers that underpin this local-scale variation in forest dynamics remain poorly understood. Here we used repeat airborne laser scanning data acquired across >1500 ha of old-growth tropical forest in Malaysian Borneo to explore how soils and topography influence rates of gap formation, closure and canopy growth across the landscape. We found that both canopy gains and losses were 2.5–4.7 times greater in low-lying alluvial forests on fertile soils compared to nearby nutrient-depleted heath forests on hilltops. Moreover, we found that variation in canopy 3D structure and dynamics were tightly coupled across the landscape, with taller and more structurally heterogeneous canopies also experiencing faster rates of gap dynamics. Our study highlights the key role that soils and topography play in shaping the structural complexity and dynamics of tropical forest landscapes.