Thermal inertia, a parameter calculated from surface temperatures obtained from spacecraft, has long been used to quantify the amount of loose, fine-grained material on the Martian surface. With little “ground truth” available, studies often refer to Martian dune fields to calibrate thermal inertias. The well-understood physical properties of dune sand make it an ideal basis for comparison to more complex surfaces. However, higher-resolution data sets available from the TES (Thermal Emission Spectrometer onboard Mars Global Surveyor) and THEMIS (Thermal Emission Imaging System onboard Mars Odyssey) show spatial variations in the thermal properties within dune fields, calling into question their effectiveness as controls for thermal inertia studies. In order to explain these variations, we apply a thermal model developed for TES data to a commonly investigated dune field in Noachis Terra, that on the floor of Proctor Crater. We show that in this dune field, the thermal variations on the scale of 30 J m−2 s−0.5 K−1 are present and correlate spatially with aeolian features in the dune field. These variations correspond to three types of surfaces observed in the Mars Orbital Camera Narrow Angle (MOC NA) images: (1) dune sand, (2) interdunes exposing the surface underlying the dune field, and (3) sand-covered interdunes, or dune troughs. Both the interdunes and the dune troughs have cooler nighttime temperatures than the dune sand, corresponding to lower thermal inertia values. The dune troughs may be sand-covered areas with either minor amounts of dust accumulation or a mean sand grain size lower than that of dune sand. Because fine sand grains tend to preferentially accumulate on dune crests rather than in dune troughs, the second hypothesis is considered less likely than the first. This has implications for the recent sedimentary history of the dune field: Dust accumulation in dune troughs may imply that sand saltation is not prevalent enough to scour away all of the dust settling out from suspension in the atmosphere; however, it is prevalent enough to keep the dunes crests themselves clear of dust.