Neurotoxic methylmercury (MeHg) formed from inorganic divalent mercury (Hg(II)) accumulates in aquatic biota and remains at high levels worldwide. It is poorly understood to what extent different geochemical Hg pools contribute to these levels. Here we report quantitative data on MeHg formation and bioaccumulation, in mesocosm water-sediment model ecosystems, using five Hg(II) and MeHg isotope tracers simulating recent Hg inputs to the water phase and Hg stored in sediment as bound to natural organic matter or as metacinnabar. Calculations for an estuarine ecosystem suggest that the chemical speciation of Hg(II) solid/adsorbed phases control the sediment Hg pool's contribution to MeHg, but that input of MeHg from terrestrial and atmospheric sources bioaccumulates to a substantially greater extent than MeHg formed in situ in sediment. Our findings emphasize the importance of MeHg loadings from catchment runoff to MeHg content in estuarine biota and we suggest that this contribution has been underestimated.