The speciation of mercury (Hg) in Minamata Bay (Japan) was studied over a 2-year period (2006)(2007)(2008). Concentrations of dissolved total Hg, dissolved methylmercury (MeHg), particulate total Hg, and suspended solids were 0.43±0.14 ng/l (mean±standard deviation), 0.10±0.06 ng/l, 3.04±2.96 ng/l, and 5.94± 2.10 mg/l, respectively. Correlations between concentrations of particulate total Hg and suspended solids at four depths (surface: 0 m; mid-depth: −6 m, −10 m; and bottom +1 m layer) were only significant in the bottom +1 m layer. The mean dissolved MeHg concentration and the ratio of dissolved MeHg to dissolved total Hg were considerably higher in summer compared to other seasons. The data suggest that bottom sediment was not the sole source of MeHg, and that MeHg may be produced in the water column by the conversion of divalent Hg eluted from resuspended bottom sediment. The correlation between seawater characteristics such as salinity, temperature, dissolved oxygen (DO), and dissolved MeHg concentration indicates that Hg methylation could be influenced by the heterotrophic activity of microorganisms in the seawater. In particular, inverse correlations were observed between DO, salinity, and MeHg concentration. However, dissolved MeHg concentrations did not correlate with seawater characteristics such as pH or chlorophyll-a.