This study discovers various geothermal prospects in the Great Basin, USA based on shallow groundwater chemical (geochemical) data. The geochemical data are expected to include hidden (latent) information that is a proxy for geothermal prospectivity. We processed the sparse geochemical data in the Great Basin at 14,341 locations including 18 attributes. Next, a non-negative matrix factorization with customized k-means clustering (NMFk) is applied to the geochemical data matrix. NMFk automatically finds three hidden geothermal signatures representing modestly, moderately, and highly confident geothermal prospects. The algorithm also evaluated the probability of occurrence of these types of resources through the studied region. There is a consistency between regional geothermal prospectivity as estimated by our ML methodology and the traditional play fairway analysis conducted over a portion of the study area. We also identify the dominant data attributes associated with each signature. Finally, our ML analyses allow us to reconstruct attributes from sparse into continuous over the study domain. The predicted continuous attributes can be used for future detailed geothermal explorations in the Great Basin.