Here, we present a model for the prediction of nanoparticle fate in aquatic environments, parametrized using functional assays that take into account conditions of the environmental media and nanoparticle properties. The model was used to explore scenarios for five nanomaterials in a freshwater wetland setting and compared with experimental results obtained in mesocosm studies. Material characteristics used in the model were size, density, dissolution rate constants, and surface attachment efficiencies. Model predictions and experimentally measured removal rate constants from the water column were strongly correlated, with Pearson correlation coefficient 0.993. Further, the model predicted removal rate constants quantitively very close to measured rates. Of particular importance for accurate predictions were two key processes beyond the usual heteroaggregation with suspended solids. These were homoaggregation of nanomaterials and nanomaterial attachment to aquatic plant surfaces. These results highlight the importance of including all relevant aggregation and deposition processes over short time scales for nanoparticle transport, while demonstrating the utility of functional assays for surface attachment as model inputs.