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We evaluated variation in dissolved organic matter (DOM) export as a function of hydrology and land use from a large arid river basin in northwestern China. Two soil-derived, humic-like (C1 and C2) and three protein-like fluorescence components (C3, C4, and C5) were identified. During high discharges, river water DOM had higher values of DOC concentration, percent humic fluorescence, and humification index, but lower values of fluorescence index and percent protein fluorescence than found at base flow, suggesting that flow paths shifted to shallower depths flushing out topsoil organic matter. Loading of DOC and soil-derived humic fluorescence were driven largely by discharge, with values over 10 times higher during high discharges than at base flow. Furthermore, both C-13-DOC and C1 at high flows positively correlated with %agricultural lands within 1km river buffers, demonstrating that near-river agricultural activities enhanced storm export of soil DOM. At base flow, C4 positively correlated with %agricultural lands, showing stimulation of aquatic bacterial carbon production as a result of elevated nutrient inputs from agricultural lands. Percent contributions of humic fluorescence in groundwater varied with well depths in shallow wells, but this pattern was not observed for deeper groundwater, suggesting that humic DOM could serve as a water source tracer indicating deeper aquifers were isolated from river water and shallow groundwater. Together, our data demonstrate that hydrology and land use controlled the sources and amount of riverine DOM in this large agricultural basin and that regulating storm runoff and near-river agricultural activities should be incorporated in ecosystem-based management of water resources.