Bioaccumulation models predict internal contaminant concentrations (ci) using ecological, chemical and physiological parameters. Here we analyse the effect of uncertainties on these parameters on bioaccumulation model predictions. Simultaneously considering the uncertainties on all these parameters in a bioaccumulation model resulted in uncertainty ranges of ci that increased with the octanol water partition coefficient Kow and reached maxima of up to 1.25 log units for mesozooplankton and up to 1.45 log units fish at log Kow=8. A global sensitivity analysis (SA) was performed to rank the contribution of different parameters to the observed uncertainty. The SA demonstrated that this interspecies difference resulted predominantly from uncertain production rates of fish. The Kow, the water concentration and organic carbon–octanol proportionality constant were important drivers of uncertainty on ci for both species. A tissue based risk quotient (RQtissue) combining uncertainty on ci with realistic tissue based effect thresholds indicated that fish were up to 10 times more probable to have RQtissue>1 than mesozooplankton, depending on the considered threshold value. Conventional exposure based risk quotients were up to 5 times less probable to exceed one than were corresponding RQtissue, and this for both species.