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Bulrushes of the genus Bolboschoenusare robust, ecologically important sedges occurring in wetlands, including intertidal marshes and mudflats. Despite their importance and multiple serious threats to their habitats, estuarine Bolboschoenusspecies remain poorly known. We conducted herbarium and field research in order to document historic and current geographic distributions, characterize the habitats, and assess the conservation status of Bolboschoenusspecies in the Hudson River Estuary, New York, U.S.A. Three species of Bolboschoenusgrow in intertidal zones in the Hudson Estuary. Bolboschoenus fluviatilisoccurs in the northern, upstream, and freshwater portion of the estuary with multi-year mean surface salinities of 0.078–2.0 ppt. Bolboschoenus robustusoccupies the southernmost, downstream, and brackish to saline portion of the estuary with salinities of 4.9–16 ppt. Bolboschoenus novae-angliaeoccurs in the slightly to strongly brackish region between the other two species with salinities of 1.8–8.0 ppt. The geographic ranges of B. fluviatilisand B. robustusdo not overlap, but B. novae-angliaehas short zones of sympatry with each of the other two species. Syntopy of B. novae-angliaewith each of the other two species is rare. In the Hudson Estuary, B. fluviatilisis secure, but B. novae-angliaeand B. robustusare critically imperiled. Threats to future survival of Bolboschoenusspecies in the Hudson Estuary include competition from invasive plant species (especially Phragmites australis), eutrophication resulting from excess nutrient pollution, and habitat destruction. Our data and analyses provide critical new information for management of existing environmental problems and planned habitat restoration efforts in the Hudson River Estuary.