Floodplain soils polluted with high levels of mercury (Hg) are potential point sources to downstream ecosystems. Repeated flooding (e.g., redox cycling) and agricultural activities (e.g., organic matter addition) may influence the fate and speciation of Hg in these soil systems. The formation and aggregation of colloids and particles influence both Hg mobility and its bioavailability to microbes that form methylmercury (MeHg). In this study, we conducted a microcosm flooding–draining experiment on Hg-polluted floodplain soils originating from an agriculturally used area situated in the Rhone Valley (Valais, Switzerland). The experiment comprised two 14 d flooding periods separated by one 14 d draining period. The effect of freshly added natural organic matter on Hg dynamics was assessed by adding liquid cow manure (+MNR) to two soils characterized by different Hg (47.3±0.5 or 2.38±0.01 mg kg−1) and organic carbon (OC: 1.92 wt % or 3.45 wt %) contents. During the experiment, the release, colloid formation of Hg in soil solution and net MeHg production in the soil were monitored. Upon manure addition in the highly polluted soil (lower OC), an accelerated release of Hg to the soil solution could be linked to a fast reductive dissolution of Mn oxides. The manure treatments showed a fast sequestration of Hg and a higher percentage of Hg bound by particulate (0.02–10 µm). Also, analyses of soil solutions by asymmetrical flow field-flow fractionation coupled with inductively coupled plasma mass spectrometry (AF4–ICP–MS) revealed a relative increase in colloidal Hg bound to dissolved organic matter (Hg–DOM) and inorganic colloidal Hg (70 %–100 %) upon manure addition. Our experiment shows a net MeHg production the first flooding and draining period and a subsequent decrease in absolute MeHg concentrations after the second flooding period. Manure addition did not change net MeHg production significantly in the incubated soils. The results of this study suggest that manure addition may promote Hg sequestration by Hg complexation on large organic matter components and the formation and aggregation of inorganic HgS(s) colloids in Hg-polluted Fluvisols with low levels of natural organic matter.