The Yolo Bypass (YB) is a large flood conveyance system designed to protect the city of Sacramento, California, USA from flooding when the Sacramento River approaches flood stage. The Sacramento River watershed and YB are a source of methylmercury (MeHg) to downstream habitat as a result of historic mercury (Hg) and gold mining practices. In the dry season, the YB is extensively farmed and grazed. However, depending on the water year, the floodplain may remain inundated for months. Our experiments focused on the role of pasture land and decomposing vegetation as a source of MeHg during extensive periods of floodplain flooding. Decomposing vegetation, rather than sediment, was identified as the principal source of filter passing MeHg (fMeHg) within the floodplain. The decomposing vegetation provided a substrate for microbial methylation of inorganic Hg contained within the plants. In replicated flooded mesocosm experiments, MeHg concentrations increased from 2.78 to 31.0 ng g−1 dw and 3.41 to 56.8 ng g−1 dw in decomposing vegetation. In field collections, the concentrations of MeHg in vegetation increased from preflood levels of 2.78 to 45.4 ng g−1 dw after 17 weeks of flooding. The importance of vegetation was shown in laboratory experiments where there was a positive correlation between the amount of fMeHg in water and the amount of vegetation added. These results also provide Hg concentration data for an important functional type of vegetation, grasses, and fill a data gap that contributed to uncertainties with regards to the role of vegetation in Hg cycling.