Reporter gene, transcriptomic, and proteomic technologies have made it possible to measure active growth region, gene and protein expression in microbial biofilms. How can differences in biofilm gene expression, both in comparison to planktonic cells and in space and time within the biofilm, be understood? Here we propose a general modelling framework for addressing this question. At the core of the model are reaction-diffusion equations that account for microscale concentration gradients within the biofilm. It is these differences in local concentrations that underpin differences in local growth, gene, and protein expression. Numerical simulations of several specific cases and comparison with experimental results will be provided.