Accurate characterization of the time courses of BOLD signal changes is crucial for the analysis and interpretation of functional MRI data. While several studies have shown that white matter (WM) exhibits distinct BOLD responses evoked by tasks, there have been no comprehensive investigations into the time courses of spontaneous signal fluctuations in WM. We measured the power spectra of the resting-state time courses in a set of regions within WM identified as showing synchronous signals using independent components analysis. In each component, a clear separation between voxels into two categories was evident, based on their power spectra: one group exhibited a single peak, the other had an additional peak at a higher frequency. Their groupings are location-specific, and their distributions reflect unique neurovascular and anatomical configurations. Importantly, the two categories of voxels differed in their engagement in functional integration, revealed by differences in the number of inter-regional connections based on the two categories separately. Moreover, the power spectral measurements in voxels with two peaks in specific components predict specific human behaviors. Taken together, these findings suggest WM signals are heterogeneous in nature and depend on local structural-vascular-functional associations.