<p>Nitrate salts are critical resources for both agriculture and industry, so understanding the genesis of large deposits is of strategic importance. Nitrate deposits are typically classified into two main types based on their depositional environment: salt flat and salt lake. Previous isotopic studies have established that nitrate in the Atacama deposit, Chile, the world’s largest, and in salt flat-type deposits in Xinjiang, China, is of predominantly atmospheric origin. However, the nitrogen and oxygen isotopic signatures of the Wuzongbulake and Wuyongbulake niter deposits (salt lake type) in Xinjiang differ significantly from those of the salt flat type, suggesting an additional nitrate source. This study systematically analyzed the <i>δ</i>¹⁵N and <i>δ</i>¹⁸O values of nitrate from niter deposits and associated aqueous samples (snowmelt, fracture water, groundwater, brine, and spring water) from the Kumishi Basin, Xinjiang, to constrain these sources. The obtained results reveal that nitrate deposits (salt flat type) derive nitrate solely from atmospheric deposition. In contrast, niter deposits (salt lake type) incorporate nitrate from aqueous pathways in addition to the atmospheric contribution. This dual-source mixing model explains their contrasting isotopic signatures and provides a framework for differentiating niter deposit types in arid endorheic basins.</p>