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Defining core areas for conservation of semi-aquatic species requires data on habitat requirements and space use. Many freshwater turtles use multiple bodies of water and intervening terrestrial habitat, and there are often sex differences within populations. We use 19 years of mark-recapture data from Sonoran Mud Turtles (Kinosternon sonoriense) to evaluate core area requirements and examine intersexual differences in movements. Our study area was in the Peloncillo Mountains of southwestern New Mexico, USA, a complex desert landscape characterized by variable hydroperiods. The primary study canyon included an intermittent impoundment and 3.75 km of canyon bed where ephemeral pools formed during wet periods. Linear home ranges in the primary study canyon were over twice as long for males than females, and males were over five times more likely to undergo long-distance movements outside the primary study canyon. Apparent mortality was nearly three times greater for males, indicating that many males were transients. Catchability was low and did not differ between sexes. Both sexes underwent seasonal migrations corresponding to water availability in canyon pools. Core areas for conservation of Sonoran Mud Turtles should include impoundments connected to extensive runs of canyon pools. A core area that included the primary study canyon would encompass the known movements of 88% of the adults we encountered. To encompass 100% of known movements, maintaining connectivity of aquatic habitats on a range-wide scale is needed. In particular, likely dispersal pathways along drainages and over low points along ridges should be included in core areas.