The alligator snapping turtle (Macrochelys temminckii), the largest freshwater turtle in North America, faces numerous threats, with population declines and range contractions suspected to have occurred across its historic range. Previous research studying movement patterns and microhabitat use of M. temminckii has mostly been conducted in large, open, lentic environments and few studies have been conducted in small, lotic habitats. We investigated the movement and microhabitat use of adult female and juvenile M. temminckii within Bonaldo Creek, a small tributary of the Angelina River in eastern Texas. Six M. temminckii were monitored (two or three relocations per week) via radiotelemetry from July 2008 to September 2009. We found that the linear home range for adult females (405.1–1395.5 m) was longer than that of the unsexed juveniles (439.7–996.9 m), although movement frequency was similar between groups. Juveniles utilized a smaller subset of microhabitats compared to adult females. Adult females utilized microhabitats with abundant submerged structure, while overhanging vegetation was an important microhabitat feature for juveniles. The broader microhabitat use we observed in adult females may have been influenced by seasonal factors, highlighting the need for more long-term, seasonal assessments of M. temminckii movement and microhabitat. Such investigations will bolster our understanding of the spatial and temporal factors that influence M. temminckii populations in different systems.