AbstractThe Southern Ocean connects the ocean's major basins via the Antarctic Circumpolar Current (ACC), and closes the global meridional overturning circulation (MOC). Observing these transports is challenging because three‐dimensional mesoscale‐resolving measurements of currents, temperature, and salinity are required to calculate transport in density coordinates. Previous studies have proposed to circumvent these limitations by inferring subsurface transports from satellite measurements using data‐driven methods. However, it is unclear whether these approaches can identify the signatures of subsurface transport in the Southern Ocean, which exhibits an energetic mesoscale eddy field superposed on a highly heterogeneous mean stratification and circulation. This study employs Deep Learning techniques to link the transports of the ACC and the upper and lower branches of the MOC to sea surface height (SSH) and ocean bottom pressure (OBP), using an idealized channel model of the Southern Ocean as a test bed. A key result is that a convolutional neural network produces skillful predictions of the ACC transport and MOC strength (skill score of 0.74 and 0.44, respectively). The skill of these predictions is similar across timescales ranging from daily to decadal but decreases substantially if SSH or OBP is omitted as a predictor. Using a fully connected or linear neural network yields similarly accurate predictions of the ACC transport but substantially less skillful predictions of the MOC strength. Our results suggest that Deep Learning offers a route to linking the Southern Ocean's zonal transport and overturning circulation to remote measurements, even in the presence of pronounced mesoscale variability.