Both observations and high resolution numerical models show that the Southern Ocean circumpolar flow is concentrated in a large number (approximately 8 to 12) of narrow filamentary jets. It is shown here that coherent jets exhibit a range of low frequency variability, on timescales of months to years, that can lead to displacement and to intermittent formation and dissipation of jets. Using output from an eddy‐resolving ocean general circulation model in local regions near topographic features, the impact of energy exchange between eddy and mean flow components on jet persistence and variability is examined. A novel approach that uses a time‐dependent definition of the mean flow provides a clearer picture of eddy‐mean flow interactions in regions with spatially and temporally varying flow structure. The dynamics are largely consistent with those in idealized quasi‐geostrophic models, including topographically‐organized and surface‐enhanced Reynolds stress forcing of the mean flow. Jets form during periods of enhanced eddy activity, but may persist long after the eddy activity has decayed. Similarly, jets may evolve in a downstream sense, with jet formation localized near topography and undergoing modification in response to changing bathymetry. The evolution of both temperature and potential vorticity is used to show that the low‐frequency variability of the jets impacts water mass structure and tracer transport. This study highlights various examples of Southern Ocean dynamics that will prove difficult to capture through parameterizations in coarser climate models.