Since the onset of hydraulic gold mining in California’s Sierra Nevada foothills in 1852, the environmental damage caused by displacement and storage of hydraulic mining sediment (HMS) has been a significant ecological problem downstream. Large volumes of mercury-laden HMS from the Yuba River watershed were deposited within the river corridor, creating the anthropogenic Yuba Fan. However, there are outstanding uncertainties about how much HMS is still contained within this fan. To quantify the deep storage of HMS in the Yuba Fan, we analyzed mercury concentrations of sediment samples collected from borings and outcrops at multiple depths. The mercury concentrations served as chemostratigraphic markers to identify the contacts between the HMS and underlying pre-mining deposits. The HMS had mercury concentrations at least ten-fold higher than pre-mining deposits. Analysis of the lower Yuba Fan’s volume suggests that approximately 8.1 × 10 7 m 3 of HMS was deposited within the study area between 1852 and 1999, representing ~32% of the original Yuba Fan delivered by 19 th Century hydraulic gold mining. Our estimate of the mercury mass contained within this region is 6.7 × 10 3 kg, which is several orders of magnitude smaller than what was estimated to have been lost to the mining process. We suggest that this discrepancy is likely due to a combination of missing (yet to be found) mercury masses stored upstream, overestimated losses during mining, and high delivery of mercury to the lowland Sacramento Valley and to the San Francisco Bay-Delta system, where it poses a great risk to sensitive ecosystems.