The Cantabrian region of Northern Spain was an important area of human occupation during the Middle and Upper Palaeolithic as the rich archaeological record demonstrates. The environmental conditions experienced by late Neanderthals and Anatomically Modern Humans (AMH) in the region during MIS3 are still poorly known, but are crucial to understand the role climatic instability could have had on the adaptations of these populations. In this study, a series of archaeological levels with Mousterian and Aurignacian artefact assemblages, dating between 49 and 35 ka uncal. BP, from the sites of El Castillo and Covalejos caves in Cantabria were studied using multi-isotope techniques including bone collagen δ13C, δ15N and δ34S analysis and a pilot study based on tooth enamel δ18O and δ13C. Results at Covalejos indicate a large range in δ15N values observable within both Mousterian Level D and Aurignacian Level B, suggesting the presence of different micro-environments within the local area at certain times during each temporal period. Within Aurignacian Level C and Mousterian Level J, the δ15N values range is much smaller, but shows consistency in the parts of the landscape being exploited during both times. Neanderthals and AMH appear to have been procuring animals from isotopically similar zones (isozones) when they occupied Covalejos. The variations in δ34S values between levels analysed at Covalejos also implies the use of a variety of hunting locations by both late Neanderthals and AMH. At El Castillo, δ13C and δ15N values show great consistency between levels, indicating that animals were being hunted from the same isozones when the site was presumably occupied by the two human species. The mosaic landscapes of Cantabria may have buffered the sharp environmental fluctuations that occurred during late MIS3 throughout Europe, providing suitable habitats for the key prey ungulate species that were routinely exploited throughout the Middle and Early Upper Palaeolithic. This environmental buffering may explain why this southerly, oceanic region was consistently occupied throughout this time of bio-cultural transition.