Reservoir siltation poses a significant challenge to water resource management and ecological balance, particularly in arid regions affected by water and wind erosion. Quantifying sediment sources in reservoirs is crucial for the sustainable operation and management of reservoir systems. The Hongyashan Reservoir (HYSR), the largest desert reservoir in Asia, has experienced severe siltation due to the combined effects of fluvial and aeolian processes. However, little is known about their respective source contributions. To this end, this study quantitatively elucidates the contributions of the Shiyang River and Gobi area to the HYSR siltation based on geochemical indicators and the FingerPro mixing model, and proposes sustainable soil and water conservation strategies. Quantitative provenance identification was determined based on robust geochemical indicators using the conservativeness index (CI), consensus ranking (CR) and consistent tracer selection (CTS) methods, revealing that both fluvial and aeolian sediments are potential material sources for the HYSR siltation. The results indicate that aeolian processes contribute more to the HYSR than fluvial processes, with average contributions of 51.18% and 48.82%, respectively. The accuracy of source apportionments was validated through the goodness-of-fit (GOF) and virtual mixtures (VM) methods. The spatial distribution of source contributions within the HYSR demonstrates notable heterogeneity, with the southern region dominated primarily by fluvial sediments, while the northern area is influenced by wind-driven deposition. The spatial heterogeneity of source contributions highlights the combined influence of fluvial and aeolian processes. This study provides critical insights into sustainable water resource management in the Shiyang River Basin (SRB) and offers implications for desertification prevention and ecosystem protection in the basin. The fingerprinting method and findings presented in this study offer a transferable framework for quantifying mixed fluvial-aeolian sediment sources in arid reservoir systems globally.