To study uranium transport by surface water from Sierra Peña Blanca to Laguna del Cuervo in the Chihuahuan Desert, sediments from intermittent streams and the lagoon have been extracted and studied. Two samples are sediments from the high area of ​​the Sierra, close to the uranium deposit “El Nopal.” Moreover, 23 segments of a sedimentary core were analyzed to study changes in the fine component concentrations. The techniques of scanning electron microscopy-energy dispersive X-ray spectroscopy, XRD in a conventional diffractometer, and high-resolution synchrotron XRD analysis were applied. The crystallographic objective has been to evaluate the functionality of various methodologies when applied to cases of detailed analysis of many polyphase samples with cryptocrystals. The methods for processing the experimental data have been the Rietveld method, in the current multi-pattern variant of the Fullprof program, and the Degree of Crystallinity method for rapid estimation of the proportion of cryptocrystals in a mixture. This last technique has been developed with an Ad-Hoc software package, which has been deposited in the public repository GitLab.