The data set contains a chemical analysis of the salt species from two salt deserts showing salt polygons at the surface. The data set is used together with other data sets (which characterize the environmental conditions, surface and subsurface of the deserts) to explain the driving mechanism of salt polygon growth in salt deserts.Different salt species crystallize in spatially separated patches. These patches were visually identified and sampled. Salt samples from the salt crust were collected at two sites at Owens Lake, Central California. Samples were dried, and pulverized and their mineral composition was analyzed using quantitative XRD.Pore water was collected from the subsurface at two sites at Badwater Basin (also central California) and 10 sites at Owens Lake. Elemental composition of the pore water was analyzed using ICPOES.All samples were collected during two field campaigns in November / December 2016 and January 2018.Related to this data are also- grain size distributions of sand samples taken at the field sites at different depths (see data at https://doi.pangaea.de/10.1594/PANGAEA.910996),- pictures and videos characterizing the sites (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),- surface scans measured by TLS (see data at https://doi.pangaea.de/10.1594/PANGAEA.911233) and- temperature and humidity time-series measured during one week in late 2016 (see data at https://doi.pangaea.de/10.1594/PANGAEA.922231).