Bulrushes of the genus Bolboschoenus are robust, ecologically important sedges occurring in wetlands, including intertidal marshes and mudflats. Despite their importance and multiple serious threats to their habitats, estuarine Bolboschoenus species 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 Bolboschoenus species in the Hudson River Estuary, New York, U.S.A. Three species of Bolboschoenus grow in intertidal zones in the Hudson Estuary. Bolboschoenus fluviatilis occurs in the northern, upstream, and freshwater portion of the estuary with multi-year mean surface salinities of 0.078–2.0 ppt. Bolboschoenus robustus occupies the southernmost, downstream, and brackish to saline portion of the estuary with salinities of 4.9–16 ppt. Bolboschoenus novae-angliae occurs 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. fluviatilis and B. robustus do not overlap, but B. novae-angliae has short zones of sympatry with each of the other two species. Syntopy of B. novae-angliae with each of the other two species is rare. In the Hudson Estuary, B. fluviatilis is secure, but B. novae-angliae and B. robustus are critically imperiled. Threats to future survival of Bolboschoenus species 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.