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A GPS-based underwater videomapping system (UVMS) was used to map 45 river miles of the NPS Obed Wild and Scenic River (OBRI) river system, 81 miles of the NPS Big South Fork River and Recreation Area (BISO) river system and 16 miles of the NPS Great Smoky Mountains (GRSM) Abrams creek. The objective was to develop and utilize a system to generate landscape-scale aquatic habitat maps. The UVMS is canoe and kayak-mounted with georeferenced under and above water cameras, depth sounder, width sensors and underwater lasers. GIS river maps of substrate (modified Wentworth scale), embeddedness (EPA classification), width, depth and river characteristic (pool, riffle, run) were developed. A technique to define optimal habitat locations for endangered fish and mussel species was implemented. Habitat suitability index algorithms for endangered fish and mussel species were also developed and mapped. A GPS-based snorkel video system was used to conduct georeferenced endangered species population counts and detailed aquatic habitat maps. GIS-based video databases of the above and below water river features provide a permanent record of river conditions.