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The Commonwealth of Pennsylvania successfully negotiated a $1.75 million settlement with Ashland Oil Company for injuries to aquatic resources and recreational users resulting from the January 1988 oil spill into the lower Monongahela and upper Ohio Rivers. The commonwealth's natural resource trustee agencies reserved these funds for special studies to learn more about the aquatic resources of the impacted rivers. A project team including commonwealth agencies, consulting experts, and the Ohio River Valley Water Sanitation Commission agreed to use the framework of a geographic information system (GIS) to organize geo-referenced natural resource data spatially. This paper discusses the development of a GIS base map of a river system modified by a series of navigation dams and outlines the ecological basis of the aquatic habitat classification system. This system divides individual navigation pools into component parts along longitudinal, cross-sectional, and vertical axes. These components are then combined to delimit aquatic areas and habitat conditions to define aquatic habitat types. These habitat types will serve as the basis for making an inventory of environmentally sensitive areas; and the completed GIS will have coverages of infrastructural, monitoring/regulatory, recreational, and environmental themes. The GIS will be used by Pennsylvania agencies in the management and protection of the natural resources supported by the Ohio River and its tributaries.