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The impact of the climate drying during the Holocene within the Nile River Valley System (NRVS) has been the focus of recent debate in the archaeological community. It is argued that the increased contribution of aeolian material from the neighboring Sahara Desert during the last ~7,000 years has changed the isotope compositions of bioavailable Sr relative to the geological background and thus hinders provenance investigations of human remains within the NRVS. This study reports new trace element and strontium (Sr), neodymium (Nd), and lead (Pb) isotope compositions for a combined total of 125 samples consisting of human tooth enamel and various faunal samples from different time periods, and present-day botanical samples from 11 archaeological sites along the NRVS. The new isotope data combined with published data do not support a time-dependent increase in a Saharan aeolian bioavailable Sr component during the Holocene within the NRVS; in general, Sr isotope compositions for human enamel samples match those of their corresponding faunal matrices, and these define a similar range of isotope compositions over the various time periods. The Nd and Pb isotope compositions for human tooth enamel reported here also support the limited contribution of Saharan aeolian dust within the NVRS.