Geoarchaeological research at Baaz Rockshelter focuses on reconstructing geogenic and anthropogenic formation processes at the site and examining post-depositional alterations of the archaeological record. Baaz is set in a rockshelter at the base of a limestone cliff and its archaeological sequence includes seven layers documenting the repeated use of the site during the Upper Paleolithic and Late Natufian, including a Late Natufian house, as well as several phases of Neolithic occupation. Based on lithic, faunal, and botanical analysis, Upper Paleolithic people used the site sporadically and centered their activities on hunting. During the Late Natufian and Neolithic, occupations were also short term, but more intense. Here, we present results of a geoarchaeological investigation of the deposits and the first systematic micromorphological study of a constructed, Late Natufian floor. Throughout the sequence, the main formation process is the weathering of limestone, in addition to minor but regular aeolian input of silt-sized quartz grains and mica. Post-depositional processes are rare and include minor secondary gypsum formation in all horizons and bioturbation that is most pronounced in the upper two layers. Anthropogenic processes vary in type and intensity. The Upper Paleolithic deposits contain mostly geogenic components with rare, microscopic anthropogenic components, supporting the argument for sporadic site use during this time. The Late Natufian deposits contain the remains of a house that exhibits some characteristics typical of structures from this time period, including an artificially lowered surface, a wall, the round shape of the house and a constructed floor. The floor is composed of silty clay and shows microscopic structural alterations resulting from intensive use. The house also shows unconventional features for the Late Natufian, such as a built-in mortar, built-in hearth, and a possible ash dump. The uppermost deposits with Late Natufian and Neolithic occupation have a mixed appearance and contain pits and lenses of herbivore dung.