The lowland tapir (Tapirus terrestris) is a megaherbivore integral to ecosystem functioning in South America’s tropical landscapes but is increasingly threatened by habitat loss and fragmentation. This study assessed occupancy, detectability, and activity patterns of lowland tapirs across the Orinoquia region of Colombia. We deployed 360 camera traps over 32,000 trap-days from 2015 to 2023 across nine study areas, evaluating the influence of habitat characteristics and anthropogenic factors on tapir presence using hierarchical occupancy models. Our results revealed a naïve occupancy of 0.40 and an overall detectability of 0.46. Model-averaged estimates identified dense forest cover as a critical positive predictor of tapir occupancy (Ψ = 0.58, CI: 0.39–0.64), while proximity to water resources similarly enhanced both occupancy and detectability. Conversely, anthropogenic landscapes such as pastures negatively impacted occupancy probabilities (Ψ = 0.45, CI: 0.40–0.51), whereas crop areas, primarily those used for household consumption, showed a surprising positive association. Our findings underscore the importance of dense forests and water bodies for tapir conservation and suggest that effective management strategies must address habitat fragmentation, road expansion, and human-wildlife conflicts. Future conservation efforts should include intensive monitoring, community-based participatory approaches, and consideration of climate change impacts to ensure the long-term survival of tapir populations in this rapidly changing landscape.