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Mercury fluxes were measured during the dry and rainy seasons (2005 to 2009) at the Jaguaribe River estuary, which discharges into the Equatorial Atlantic Ocean in NE Brazil. During rainy periods, the water masses exhibited a short residence time within the estuary (0.8 days). During dry periods, seawater choked the fluvial discharge, resulting in longer residence times (3.1 days). Dissolved (< 0.7 mu m) and particulate Hg concentrations and fluxes were greater from the river to the estuary than from the estuary to the sea, producing accumulated particulate Hg in the estuary. Particulate Hg export (1.8 to 12.6 mg s(-1)) to the ocean occurred during extremely rainy periods, while dissolved Hg export was practically nonexistent during rainy periods and increased up to 0.45 mg s(-1) during dry periods. Because continental runoff in semi-arid regions is affected by land use and global climate changes, the increasing accumulation of particulate Hg in the estuaries and increasing export of dissolved Hg to the ocean are expected.