Total mercury (HgT) and monomethylmercury (MMHg) were investigated in a tropical head watershed (1 km2) of French Guiana. The watershed includes a pristine area on the hill slopes and a former gold mined flat in the bottomland. Concentrations of dissolved and particulate HgT and MMHg were measured in rain, throughfall, soil water and at three points along the stream. Samples were taken in-between and during 14 storm events at the beginning and middle of the 2005 and 2006 rainy seasons. Dissolved and particulate HgT concentrations in the stream slightly increased downstream, while dissolved and particulate MMHg concentrations were low at the pristine sub-watershed outlet (median = 0.006 ng L−1 and 1.84 ng g−1, respectively) and sharply increased at the gold mined flat outlet (median = 0.056 ng L−1 and 6.80 ng g−1, respectively). Oxisols, which are dominant in the pristine area act as a sink of HgT and MMHg from rain and throughfall inputs. Hydromorphic soils in the flat are strongly contaminated with Hg (including Hg0 droplets) and their structure has been disturbed by former gold-mining processes, leading to multiple stagnant water areas where biogeochemical conditions are favorable for methylation. In the former gold mined flat high dissolved MMHg concentrations (up to 0.8 ng L−1) were measured in puddles or suboxic soil pore waters, whereas high dissolved HgT concentrations were found in lower Eh conditions. Iron-reducing bacteria were suggested as the main methylators since highest concentrations for dissolved MMHg were associated with high dissolved ferrous iron concentrations. The connection between saturated areas and stagnant waters with the hydrographic network during rain events leads to the export of dissolved MMHg and HgT in stream waters, especially at the beginning of the rainy season. As both legal and illegal gold-mining continues to expand in French Guiana, an increase in dissolved and particulate MMHg emissions in the hydrographic network is expected. This will enhance MMHg bio-amplification and present a threat to local populations, whose diet relies mainly on fish.