The Whillans Ice Stream Ice Plain (WIP) has been slowing since at least 1963. Prior constraints on this slowdown were consistent with a constant long-term deceleration rate. New observations of ice velocity from 11 continuous and 3 seasonal GPS sites indicate the deceleration rate varies through time including on interannual time scales. Between 2009 and 2012 WIP decelerated at a rate (6.1 to 10.9 ± 2 m/yr2) that was double the multidecadal average (3.0 to 5.6 ± 2 m/yr2). To identify the causes of slowdown, we used new and prior velocity estimates to constrain longitudinal and transverse force budget models as well as a higher-order inverse model. All model results support the conclusion that the observed deceleration of WIP is caused by an increase in basal resistance to motion at a rate of 10 to 40 Pa/yr. Subglacial processes that may be responsible for strengthening the ice stream bed include basal freeze on, changes in subglacial hydrology, or increases in the area of resistant basal substrate through differential erosion. The observed variability in WIP deceleration rate suggests that dynamics in subglacial hydrology, plausibly driven by basal freeze on and/or activity of subglacial lakes, plays a key role in modulating basal resistance to ice motion in the region.