Conversion of CH3Hg+ concentrations in water to CH3Hg+ concentrations in fish tissue is critically important in characterizing Hg health risks to humans and biota in aquatic ecosystems. However, this is a challenging task due to complex biogeochemical CH3Hg+ processes that are replete with uncertainty. In the present study, the uncertainty was reduced by employing the Spreadsheet-based Ecological Risk Assessment for the Fate of Mercury (SERAFM) model and a linear relationship between logarithmic Hg concentrations and stable isotope ratios of nitrogen (d15N) in biota. By using this approach, the fate, transport, and bioaccumulation of CH3Hg+ in Sarasota Bay, FL, was modeled. Modeling results suggest that *60% of the total Hg loading (8.7 kg/year) to the Sarasota Bay in 2011 originated from atmospheric Hg deposition to the watershed with subsequent transport to the waterbody via stormwater runoff. This indicated that watershed runoff could be an important source of Hg to a bay adjacent to highly urbanized areas. In addition, our modeling results suggested that Hg runoff reduction (90%) from impervious surfaces together with lowering atmospheric Hg deposition (21/10 lg/m/ year) would be a practical approach to lower current Hg levels and associated risks to the Sarasota Bay ecosystem. Since future Hg loadings to the Bay are likely to rise from increases of atmospheric Hg deposition and watershed urbanization, it will be necessary to reduce various Hg loadings by employing appropriate implementation plans for the management of this urbanized watershed.