Habitat selection is dependent on several abiotic and biotic factors which have influence at multiple spatial scales. Dependence on specific habitat characteristics for thermoregulation could make habitat selection by herpetofauna especially subtle. Enhancing knowledge of habitat selection by herpetofauna is critical for completely understanding natural histories and improving future habitat management strategies. We conducted a year-long telemetric habitat selection study on two Northern Cottonmouth (Agkistrodon piscivorus) populations in northeast Texas. We used a use–availability approach and investigated intersexual differences at three spatiotemporal scales: home range selection within the study site (home range selection); habitat selection within the home range (macrohabitat selection); and fine-scale local habitat selection (microhabitat selection). The home range selection of both males and females exhibited selection for edges and avoidance of pasture. Males only exhibited macrohabitat selection in the summer, when they selected edge and wetland. Females did not exhibit any macrohabitat selection. Males and females selected microhabitats with thick vegetation in the spring and summer. However, in the fall, male microhabitat selection was influenced by lower temperatures and female microhabitat use appeared to be driven by parturition. Although our study suffered from small female sample size and a short time frame, we provide insight into the complex habitat selection of Cottonmouths in northeast Texas.