In the development of models for diffusion and reaction in biofilms, one often begins with the assumption that the biofilm is a continuum. This approach leads to equations for which the domain of validity is not clearly defined, and it provides no theoretical foundation for the prediction of the effective coefficients that appear in the postulated equations. In this paper we treat the intracellular phase and the extracellular phase as continua and use the method of volume averaging to develop the spatially smoothed transport equations for diffusion and reaction in biofilms. This allows us to identify three regimes in which the spatially smoothed transport equations take on special forms. The first of these is the one-equation model that is valid when the principle of local mass equilibrium is satisfied; the second is the two-equation model that is not constrained by the principle of local mass equilibrium; and the third is a pseudo one-equation model. The latter occurs when the reaction in the intracellular phase can be treated as instantaneous. Constraints that identify the domain of validity of these three models are given.