Through a combination of laboratory experiments and theoretical models, we investigate the interaction of a mean upwelling through a closed basin with a vertical buoyancy flux. The fluid is mixed by a horizontally oscillating rake, which either traverses the whole basin or which oscillates just near one vertical boundary. We first review the steady state and demonstrate that, in both mixing regimes, the vertical density profile across the basin is controlled by the steady-state balance between the upward advective and diffusive fluxes of salinity as described by the classical model introduced by Munk (Deep-Sea Res., vol. 13, issue 4, 1966, pp. 707–730). However, with boundary mixing, we show that both the upwelling and the buoyancy transport are localised to the mixing zone near the boundary, and the interior fluid is stagnant. We then develop a model to describe the transient evolution of the system if there is either a discrete increase or gradual decrease to the buoyancy flux. In the boundary mixing case, the change in the buoyancy flux at the lower boundary leads to a change in the buoyancy of the fluid in the boundary mixing region, and this induces a transient, buoyancy-driven flow in the boundary region in addition to the steady upwelling. In turn, an equal and opposite vertical flow develops in the interior, and this leads to a change in the density stratification of the interior fluid as the system adjusts to a new equilibrium. However, in our experiments, there is no vertical mixing in the interior and interior fluid may upwell or downwell dependent on the change to the buoyancy forcing. We discuss the implications of our results for the transport and mixing in the deep ocean, and the associated interpretation of field experiments.