Landscape modifications often undermine habitat suitability for species' persistence, with initial effects observed through the physiological responses of individuals and populations. However, some landscape features can allow tolerant wildlife species to persist in human‐modified landscapes, but they are still overlooked. Across distinct agricultural landscapes, we assessed landscape features affecting the body condition (estimate through scaled mass index ‐ SMI) of Caiman crocodilus (Crocodylia, Alligatoridae) in human‐modified landscapes of the Araguaia floodplain, central Brazil. We used a spatial Bayesian model averaging approach to determine the effects of landscape attributes, ectoparasites, tail damage and severe body injuries on caiman body condition. We found that caimans had higher SMI in anthropogenic (ditches and artificial ponds) than natural habitats (lakes or rivers). Overall, caiman SMI was negatively associated with wetland cohesion (an aggregation and connectivity metric). Otherwise, landscape composition did not influence caiman SMI. Further, ectoparasites and body injuries did not affect SMI, whereas tail damage negatively affected SMI. Our findings underscore that caiman populations can adapt to artificial wetlands and irrigated rice fields, provided they incorporate natural and semi‐natural habitat patches that enhance environmental heterogeneity, prey availability, and waterbody availability and connectivity. [ABSTRACT FROM AUTHOR]