A model is developed for the adjustment of the spatially averaged time-mean flow of a deep turbulent boundary layer over small roughness elements to a canopy of larger three-dimensional roughness elements. Scaling arguments identify three stages of the adjustment. First, the drag and the finite volumes of the canopy elements decelerate air parcels; the associated pressure gradient decelerates the flow within an impact region upwind of the canopy. Secondly, within an adjustment region of length of order $L_c$ downwind of the leading edge of the canopy, the flow within the canopy decelerates substantially until it comes into a local balance between downward transport of momentum by turbulent stresses and removal of momentum by the drag of the canopy elements. The adjustment length, $L_c$, is proportional to (i) the reciprocal of the roughness density (defined to be the frontal area of canopy elements per unit floor area) and (ii) the drag coefficient of individual canopy elements. Further downstream, within a roughness-change region, the canopy is shown to affect the flow above as if it were a change in roughness length, leading to the development of an internal boundary layer. A quantitative model for the adjustment of the flow is developed by calculating analytically small perturbations to a logarithmic turbulent velocity profile induced by the drag due to a sparse canopy with $L/L_c \ll 1$, where $L$ is the length of the canopy. These linearized solutions are then evaluated numerically with a nonlinear correction to account for the drag varying with the velocity. A further correction is derived to account for the finite volume of the canopy elements. The calculations are shown to agree with experimental measurements in a fine-scale vegetation canopy, when the drag is more important than the finite volume effects, and a canopy of coarse-scale cuboids, when the finite volume effects are of comparable importance to the drag in the impact region. An expression is derived showing how the effective roughness length of the canopy, $\z0eff$, is related to the drag in the canopy. The value of $\z0eff$ varies smoothly with fetch through the adjustment region from the roughness length of the upstream surface to the equilibrium roughness length of the canopy. Hence, the analysis shows how to resolve the unphysical flow singularities obtained with previous models of flow over sudden changes in surface roughness.