The data set contains information about sand grain sizes of salt deserts showing salt polygons at the surface. The data set characterizes the subsurface of the salt deserts and is used together with other data sets (which characterize the surface) to explain the driving mechanism of salt polygon growth in salt deserts.The subsurface is characterized by grain size distributions of samples taken from different depths between 5 cm and 100 cm below the salt crust. Grain size distributions were measured with a laser particle sizer. Samples were not treated with ultrasound previous to measurement. The distributions supplied in the data set are averages over 3 consecutive measurements for every sample.Samples were taken at 5 sites at Badwater Basin and 21 sites at Owens Lake - both Central California. All data was recorded during two field campaigns in November / December 2016 and January 2018.Related to this data are also- images, characterizing each site (see data at https://doi.pangaea.de/10.1594/PANGAEA.911054),- salinity profiles from cross-sections below polygons and background salt concentration measurements (see data at https://doi.pangaea.de/10.1594/PANGAEA.922264),- temperature and humidity time-series measured during one week in late 2016 (see data at https://doi.pangaea.de/10.1594/PANGAEA.922231),- as well as surface scans measured by TLS (see data at https://doi.pangaea.de/10.1594/PANGAEA.911233)- and a chemical characterization of the salt species present in the crust (see data at https://doi.pangaea.de/10.1594/PANGAEA.911239).