In a 2012 study, no age-0 muskellunge (Esox masquinongy) were found in any of 16 historic nursery sites in coastal marshes of southeastern Georgian Bay (SEGB), and this was attributed to sustained low water levels (1999–2013) that had altered the vegetation structure of nursery habitat. In the same study, age-0 muskellunge were found in 16 coastal marshes surveyed in northern Georgian Bay (NGB), even though these sites had been subjected to the same water-level conditions. We hypothesize that hydrogeomorphic features of NGB sites made them resilient to effects of sustained low lake levels that made the SEGB sites unsuitable for age-0 muskellunge. Compared to their SEGB counterparts, the NGB nursery sites were significantly steeper, deeper, and less sheltered under low water levels. We used these hydrogeomorphic features to develop a multi-scale Resilience Index (RI) for identifying coastal wetlands that are resilient to stable low lake levels. The RI correctly classified the NGB and SEGB nursery sites, with an area-under-the-curve score of 0.973. Coarser-scale variants of the RI provide a regional screening tool in the identification of resilient wetland habitat (e.g. potential muskellunge nursery habitat), and a basin-wide approach to identify vulnerable wetland habitats. This multi-scale index, in conjunction with targeted field surveys, should provide managers a useful tool in the face of uncertain water level forecasts.