Great attention has been drawn to the impacts of habitat deforestation and fragmentation on wildlife species richness. In contrast, much less attention has been paid to assessing the impacts of chronic anthropogenic disturbance on wildlife species composition and behaviour. We focused on natural small rock pools (sartenejas), which concentrate vertebrate activity due to habitat’s water limitation, to assess the impact of chronic anthropogenic disturbance on the species richness, diversity, composition, and behaviour of medium and large-sized birds and mammals in the highly biodiverse forests of Calakmul, southern Mexico. Camera trapping records of fauna using sartenejas within and outside the Calakmul Biosphere Reserve (CBR) showed that there were no effects on species richness, but contrasts emerged when comparing species diversity, composition, and behaviour. These effects differed between birds and mammals and between species: (1) bird diversity was greater outside the CBR, but mammal diversity was greater within and (2) the daily activity patterns of birds differed slightly within and outside the CBR but strongly contrasted in mammals. Our study highlights that even in areas supporting extensive forest cover, small-scale chronic anthropogenic disturbances can have pervasive negative effects on wildlife and that these effects contrast between animal groups.