A conspicuous feature of the Western Antarctic Peninsula (WAP) continental shelf is the presence of deep submarine canyons that extend from the shelf break to the land margin, where during summer large colonies of breeding Adélie penguins occur. This coupled spatial association between canyons and the distribution of penguin colonies has led to the hypothesis that unique physical and biological processes induced by these canyons produce regions of enhanced prey availability that are predictable over ecological time scales (decades to centuries), or the scales needed for penguin colonies to develop following initial site occupation by founder populations. During the PAL January 2009 summer cruise we had an opportunity to investigate a component of this hypothesis, namely, that the presence of incipient colonies are indicative of deep bathymetry and canyon-induced dynamics. Our results demonstrate that on Charcot Island in the largely unexplored southern margin of the PAL LTER grid, small, previously undiscovered breeding colonies of Adélie penguins were indeed located at sites adjacent to a deep canyon complex. This canyon was formerly unknown. Data based on satellite telemetry, moreover, also showed that penguin foraging locations were closely spaced near the land margin where bathymetrically induced upwelling likely enhanced prey availability. These findings have many implications to hypotheses being explored by PAL regarding the mechanistic processes that link WAP marine ecosystem dynamics and the possible consequences of rapid climate warming to ecosystem structure and function.