This study analyses budgets of second-order turbulence moments over a real urban canopy using large-eddy simulation (LES). The urban canopy is representative of the City of Boston, MA, United States and is characterized by a significant height variability relative to the mean building height. The budgets of double-average Reynolds-stress components, scalar fluxes, and scalar variances are examined with a focus on the importance of the dispersive terms above the mean building height. Results reveal the importance of the wake (dispersive) production term, in addition to the shear production term, in the turbulent kinetic energy, streamwise velocity variance and scalar variance budgets well above the mean building height. In this region, the turbulent and dispersive transport terms are smaller than the local production and dissipation terms. Nonetheless, the dispersive transport terms in the TKE and scalar variance budgets can be as important as their turbulent counterpart. The viscous dissipation term is the main sink in the TKE, vertical velocity variance and scalar variance budgets. In the momentum and scalar flux budgets, the pressure-strain correlation term and the pressure gradient-scalar interaction term are the significant sink terms, respectively. Our analysis highlights the complexity associated with the budgets of second-order turbulence moments over real urban canopies.