The Indian subcontinent is the primary wintering ground and stopover site for migratory shorebirds to refuel along the Central Asian and South Asian Flyways. Despite the conservation importance of this region for migratory shorebirds, we lack information on the distribution and abundance of over-summering shorebirds—migrants that remain on their wintering grounds during the breeding season—to evaluate the impacts of anthropogenic change on this poorly understood life history strategy. We conducted weekly surveys of over-summering shorebirds at mudflats, mangroves, and sand beaches at the Kadalundi-Vallikkunnu Community Reserve on the southwest coast of India, 2005–2018. We examined long-term patterns of over-summering shorebird abundance, species composition, and habitat use and estimated proportional changes in over-summering abundance of each shorebird species documented at this globally important site. Over the 14 yr study, we documented 7 over-summering species, including Lesser Sand Plover (Charadrius mongolus), Whimbrel (Numenius phaeopus), Greater Sand Plover (Charadrius leschenaultia), Kentish Plover (Charadrius alexandrinus), Common Sandpiper (Actitis hypoleucos), Ruddy Turnstone (Arenaria interpres), and Pacific Golden-Plover (Pluvialis fulva). Mean abundance and species richness were higher at mudflats than at mangroves and sand beaches, with fewer individuals and species observed over-summering after 2010. Mudflats also had the highest species diversity and evenness compared to mangroves and sand beaches. Management plans that aim to restore vulnerable mudflats and mangroves and to reduce anthropogenic threats such as sand mining and waste dumping are needed to prevent the loss of important over-summering, foraging habitat for migratory shorebirds in southern India and along the Central Asian and South Asian Flyways.