The Carson River is a vital water resource for local municipalities and migratory birds travelling the Pacific Flyway. Historic mining practices that used mercury (Hg) to extract gold from Comstock Lode ore has left much of the river system heavily contaminated with Hg, a practice that continues in many parts of the world today. Between 1998 and 2013, the United States Geological Survey (USGS) collected and analyzed Carson River water for Hg and methylmercury (MeHg) concentrations resulting in a sixteen year record of unfiltered total mercury (uf.THg), filtered (dissolved) Hg (f.THg), total methylmercury (uf.MeHg), filtered MeHg (f.MeHg), and particulate-bound THg (p.THg) and MeHg (p.MeHg) concentrations. This represents one of the longest continuous records of Hg speciation data for any riverine system, thereby providing a unique opportunity to evaluate long-term trends in concentrations and annual loads. During the period of analysis, uf.THg concentration and load trended downward at rates of −0.85% and −1.8% per year, respectively. Conversely, the f.THg concentration increased at a rate of 1.7% per year between 1998 and 2005, and 4.9% per year between 2005 and 2013. Trends in flow-normalized partition coefficients for both Hg and MeHg suggest a statistically significant shift from the particulate to the filtered phase. The upwardly accelerating f.THg concentration and observed shift from the solid phase to the aqueous phase among the pools of Hg and MeHg within the river water column signals an increased risk of deteriorating ecological conditions in the lower basin with respect to Hg contamination. More broadly, the 16-year trend analysis, completed 140 years after the commencement of major Hg releases to the Carson River, provides a poignant example of the ongoing legacy left behind by gold and silver mining techniques that relied on Hg amalgamation, and a cautionary tale for regions still pursuing the practice in other countries.