The Southern Ocean (SO) is a crucial region for the global ocean uptake of heat and carbon. There are large uncertainties in the observations of fluxes of heat and carbon between the atmosphere and the ocean mixed layer, which lead to large uncertainties in the amount entering into the global overturning circulation. In order to better understand where and when fluxes of heat and momentum have the largest impact on near‐surface heat content, we use an adjoint model to calculate the linear sensitivities of heat content in SO mode water formation regions to surface fluxes. We find that the heat content of these regions is, in all three basins, most sensitive to same‐winter, local heat fluxes, and to local and remote wind one to eight years (the maximum lead‐time of our simulations) previously. This is supported by sensitivities to potential temperature changes, which reveal the sources of the mode water formation regions as well as dynamic links with boundary current regions and the Antarctic Circumpolar Current. We use the adjoint sensitivity fields to design a set of targeted perturbation experiments, allowing us to examine the linear and non‐linear responses of the heat content to changes in surface forcing. In these targeted experiments, the heat content is sensitive to both temperature changes and mixed layer volume changes in roughly equal magnitude.