A stochastic method for evaluating the in situ mass balance of micropollutants in a stormwater biofilter, accounting for inlet and outlet loads and the evolution of pollutant mass in the filter media (ΔMsoil) at an annual scale, is proposed. In the field context, this type of calculation presents a number of methodological challenges, associated with estimating water quality for unsampled rain events, reconstituting missing or invalidated flow data and accounting for significant uncertainties associated with these estimations and experimental measurements. The method is applied to a biofiltration swale treating road runoff for two trace metals, Cu and Zn and six organic micropollutants: pyrene (Pyr), phenanthrene (Phen), bisphenol-A (BPA), octylphenol (OP), nonylphenol (NP) and bis(2-ethylhexyl) phthalate (DEHP). Pollutant loads were reduced by 27–72%. While organic micropollutants are likely to be lost to degradation or volatilization processes in such systems, dissipation could not be demonstrated for any of the organic micropollutants studied due to emissions from construction materials (case of BPA, OP, NP and DEHP) or high uncertainties in ΔMsoil (case of Pyr and Phen). The necessary conditions for establishing an in situ mass balance demonstrating dissipation, which include acquisition of data associated with all terms over a period long enough that uncertainty propagation is limited and the absence of additional sources of pollutants in the field, are discussed.