Palmer Deep (PD) is one of several regional hotspots of biological productivity along the inner shelf of the West Antarctic Peninsula. The proximity of hotspots to shelf-crossing deep troughs has led to the ‘canyon hypothesis’, which proposes that circumpolar deep water flowing shoreward along the canyons is upwelled on the inner shelf, carrying nutrients including iron (Fe) to surface waters, maintaining phytoplankton blooms. We present here full-depth profiles of dissolved and particulate Fe and manganese (Mn) from eight stations around PD, sampled in January and early February of 2015 and 2016, allowing the first detailed evaluation of Fe sources to the area’s euphotic zone. We show that upwelling of deep water does not control Fe flux to the surface; instead, shallow sediment-sourced Fe inputs are transported horizontally from surrounding coastlines, creating strong vertical gradients of dissolved Fe within the upper 100 m that supply this limiting nutrient to the local ecosystem. The supply of bioavailable Fe is, therefore, not significantly related to the canyon transport of deep water. Near shore time-series samples reveal that local glacial meltwater appears to be an important Mn source but, surprisingly, is not a large direct Fe input to this biological hotspot.