The main objective of this work is to develop an overall mass transfer model applicable to a particular case of membrane supported biofilm, the ion-exchange membrane bioreactor (IEMB). A multivariate projection to latent structures (PLS) model of the anionic membrane transport in an IEMB was developed and analyzed to establish the mass transfer limiting variables for the removal of anionic pollutants (nitrate and perchlorate) from drinking water. The proposed PLS model accounts for the biological contribution to the mass transfer and predicts the anionic fluxes across the ion-exchange membrane with a prediction improvement of at least 50% when compared with a simplified mechanistic Donnan dialysis-based transport model. The PLS model allowed for predicting the transport of target anions using only operational physicochemical data, therefore, the use of several assumptions as in mechanistic model building was avoided as well as the need for biofilm characterization. To decrease the model complexity, several techniques which select the most informative predictors were also successfully used. The analyses of important predictors to each anionic transport model show that transport driving force related variables were the most important. Moreover, at least 30% of the model information is related with biocompartment bulk variables.