We anticipate noise from the Laser Interferometer Space Antenna (LISA) will exhibit nonstationarities throughout the duration of its mission due to factors such as antenna repointing, cyclostationarities from spacecraft motion, and glitches as highlighted by LISA Pathfinder. In this paper, we use a surrogate data approach to test the stationarity of a time series which does not rely on the Gaussianity assumption. The main goal is to identify noise nonstationarities in the future LISA mission. This will be necessary for determining how often the LISA noise power spectral density (PSD) will need to be updated for parameter estimation routines. We conduct a thorough simulation study illustrating the power/size of various versions of the hypothesis tests and then apply these approaches to differential acceleration measurements from LISA Pathfinder. We also develop a data analysis strategy for addressing nonstationarities in the LISA PSD, where we update the noise PSD over time, while simultaneously conducting parameter estimation, with a focus on planned data gaps.