This paper investigates the aqueous geochemistry of mercury (Hg) in three aquatic systems impacted by either past or present mining activities. The Idrija River in Slovenia flows near the Idrija mercury mine, the second largest mercury mine in the world, with continuous mining and smelting activities for five centuries. During this period, it has been estimated that over 30 000 tonnes of Hg have been released into the mine's surrounding environment, due to inefficient smelting technologies and Hg left behind in mine tailings within the river basin. In contrast to cinnabar mining in the Idrija River Basin, the Carson River in Nevada and the Madeira River in the Brazilian Amazon are impacted by metallic mercury (Hg0) used in the amalgamation process to extract gold (Au) and/or silver (Ag) from crude ores and fine alluvial materials. The Carson River Basin was the site of intensive Au- and Ag-mining for over 50 years in the late 1800s and early 1900s, resulting in an estimated 7000 tonnes of Hg lost to the river and its watershed. The Madeira River is a site of ongoing use of Hg0 in Au-prospecting. This study reports on the level and speciation of Hg, as well as factors controlling levels of methyl-Hg using aqueous data. Surface water samples collected along longitudinal transects upstream of well-identified point sources of Hg, except for the Madeira River, to river deltas were analysed for Hg and geochemical parameters of interest. Samples from Idrija and Carson rivers show clear evidence of contamination, with Hg levels up to several hundreds of ng l−1 downstream from main point sources. Unlike Idrija and the Carson rivers, water samples collected from the Madeira River exhibited much lower Hg levels (9.51 ng l−1 on average, n = 16). Measured physiochemical parameters are used to determine the fate of Hg in these three river systems.