Building a regional GIS requires integrated tools and techniques. The Bay Area EcoAtlas is a geographic information system of past and present local ecology of the bays, bay lands, and adjacent habitats of the San Francisco Bay area. It is designed to support regional environmental planning and management. The EcoAtlas was developed with a wide selection of database, GIS, and graphics software on multiple operating systems functioning in a collaborative mix of science, government, and public participation. Critical challenges (historical map compilation and registration, truthing, presentation, data exchange, and documentation) were overcome using a combination of standard and custom processes.