A hydrographic survey offshore Ningaloo reef, north-west Australia, in austral autumn 2010 revealed relatively stable subsurface water masses in the region, despite the influence of interannual variability of the Leeuwin Current (LC). The surface water mass seems slightly more variable at seasonal time scale, probably due to various contributions of the geographically distinct source waters of the LC. A subsurface nitrate maximum (~110–230 m), a prominent feature of the Ningaloo area during autumn, was consistently observed within different water masses. Tightly coupled variations of subsurface nitrate and oxygen at small vertical scale suggest it is due to local in situ remineralization of organic matter likely to accumulate along sharp physical interfaces and possibly favored by injections of oxygenated subsurface waters. Offshore, enhanced levels of surface chlorophyll a within the downwelling-favorable LC are associated with deeper mixed layer depth, eroding the shallow source of nutrients. Close to the continental shelf, these nutrients are observed to be efficiently uplifted within the core of quasi-persistent topographically trapped submesoscale cyclonic eddies dominated by nonlinear effects. A wind-driven coastal upwelling event occurred in autumn and was characterized by a relatively deep source (~100–150 m), coinciding with the subsurface maximum of nutrients, thus promoting coastal productivity locally and farther north by alongshore advection within the Ningaloo current.