We studied bats in a natural protected area and the influence zone in Chiapas, México. Focusing on small vesper bats (Vespertilionidae: Myotinae) in water sinkholes, flooded surfaces, and forested locations (sampling sites), our objectives were to: 1) differentiate the sampling sites based on abiotic and biotic variables, 2) compare the relative activity between the contrasting sampling sites, and 3) determine the relative importance of surrounding land covers amounts on the relative activity. We expected the following: 1) that sampling sites would be differentiable based on an interaction of environmental conditions and nocturnal flying insects’ biomass, 2) to find a significantly higher relative activity associated with water bodies as a reflection of potential drinking and feeding supplies, and 3) that forest cover would have a significant association in a positive direction with the relative activity as a reflection of roosting and commuting opportunities. We obtained weather data with a portable station, collected flying nocturnal insects with a passive trap, and recorded bats with ultrasonic detectors. We also used satellite imagery to calculate land covers amounts around the sampling sites. We performed a multivariate analysis to compare sampling sites, and elaborated correlation models of relative activity against surrounding land covers amounts. The only significant variable for differentiating sampling sites was wind speed; in water sinkholes, with lower mean value compared to flooded surfaces and forested locations, along with a comparatively higher percentage of dipterans in the samples. The mean relative activity of bats was significantly higher in water sinkholes, with maximum values reaching 95 %, which we can relate to environmental conditions and resources available. We found associations in a positive direction with forest cover, secondary forest and water surface, and negative with agricultural land and human development. Finally, we argue that some of the water sinkholes meet the criteria of small natural features supported by the unusual activity of the studied bats, and that targeted conservation actions will complement other strategies implemented in the area.