Salt marshes are vulnerable to climate change-associated sea-level rise and storm-induced surges. Their degradation will likely affect shorebirds relying on this ecosystem. Least Sandpiper (Calidris minutilla) and Pectoral Sandpiper (Calidris melanotos) migrating along coastline habitats typically use salt marshes to rest and replenish their body reserves. Our objective was to test if width of the different vegetation zones within salt marshes affects the occurrence of Least and Pectoral Sandpipers stopping along the St. Lawrence River Estuary, Quebec, Canada, during fall migration. We established 26 survey sites, each 600 m in length, along the shoreline. Shorebird surveys were conducted in 2011 and 2012. We characterized salt marshes by measuring the width of each vegetation zone (lower marsh and upper marsh). We analyzed shorebird presence/not detected data with generalized estimating equations to test the predictions that occurrence of Least Sandpipers and Pectoral Sandpipers increases with width of both the lower and upper marsh. Upper marsh width was positively associated with probability of occurrence in each species. Our results highlight the importance of protecting the integrity of salt marshes for these two species. In the St. Lawrence River Estuary, where landward migration of salt marshes is no longer possible (coastal squeeze), effective management of shorelines is much needed. Otherwise, salt marshes and these two species could be locally jeopardized.