Submerged aquatic vegetation (SAV) is widely recognized as an important habitat and indicator of water quality in large rivers and estuaries. Despite the perceived importance, system-wide assessments of cover, susceptibility to change, and ecological functioning are rare because of the geographical scope and multi-disciplinary expertise required. A collaboration between scientists, estuarine managers, and environmental educators was initiated to map the SAV and the Eurasian water chestnut (Trapa natans) in the Hudson River estuary from Hastings-on-Hudson north to Troy, New York. These groups provided diverse scientific and estuarine management expertise to enable the first broad delimitation of SAV in the Hudson and sampling of beds to describe abundance, biomass, and species composition and to address management and education needs and opportunities. The areal extent of SAV based on a combination of 1995 and 1997 photographs in the study area was 1,802 hectares (4,453 acres), ∼6% of the river area and ∼18% of the shallows (defined as less than 3 meters deep at low tide). Trapa natans covered 575 hectares (1,421 acres), 2% of the river area and 6% of the shallows. In the most heavily vegetated portion of the Hudson (approximately 150–200 kilometers of river), the coverage by plants (both SAV and T. natans) approached 25% of the river bottom area. Results of this work have been integrated into the federal and state regulatory processes, local resource users, and local science education programs. Finally, we have initiated a volunteer SAV monitoring program.