Solid-liquid partitioning is one of the main fate processes determining the removal of micropollutants in wastewater. Little is known on the sorption of micropollutants in biofilms, where molecular diffusion may significantly influence partitioning kinetics. In this study, the diffusion and the sorption of 23 micropollutants were investigated in novel moving bed biofilm reactor (MBBR) carriers with controlled biofilm thickness (50, 200 and 500 μm) using targeted batch experiments (initial concentration = 1 μg L−1, for X-ray contrast media 15 μg L−1) and mathematical modelling. We assessed the influence of biofilm thickness and density on the dimensionless effective diffusivity coefficient f (equal to the biofilm-to-aqueous diffusivity ratio) and the distribution coefficient Kd,eq (L g−1). Sorption was significant only for eight positively charged micropollutants (atenolol, metoprolol, propranolol, citalopram, venlafaxine, erythromycin, clarithromycin and roxithromycin), revealing the importance of electrostatic interactions with solids. Sorption equilibria were likely not reached within the duration of batch experiments (4 h), particularly for the thickest biofilm, requiring the calculation of the distribution coefficient Kd,eq based on the approximation of the asymptotic equilibrium concentration (t > 4 h). Kd,eq values increased with increasing biofilm thickness for all sorptive micropollutants (except atenolol), possibly due to higher porosity and accessible surface area in the thickest biofilm. Positive correlations between Kd,eq and micropollutant properties (polarity and molecular size descriptors) were identified but not for all biofilm thicknesses, thus confirming the challenge of improving predictive sorption models for positively charged compounds. A diffusion-sorption model was developed and calibrated against experimental data, and estimated f values also increased with increasing biofilm thickness. This indicates that diffusion in thin biofilms may be strongly limited (f ≪ 0.1) by the high biomass density (reduced porosity).