Florida's coasts have been transformed over the past three decades as population growth and unprecedented demand for individual shore access to bays and estuaries led to the creation of residential canal developments. Thousands of miles of channels and basins were dredged as a by-product of this urbanization process. The navigable waterways that resulted are now being stressed by increasing boat traffic and canal-side activities. Recognizing their common goal to preserve the recreational and ecological value of southwest Florida waterways, the Florida Department of Environmental Protection, the four-county West Coast Inland Navigation District, and the University of Florida Sea Grant College Program signed a Memorandum of Agreement. The signatories agreed to develop a science-based Regional Waterway Management System (RWMS), which is a new approach to waterway planning and permitting based on carefully mapped channel depths, a census of actual boat populations, and the spatial extent of natural resources. The RWMS provides a comprehensive, regional overview of channel conditions and the geographic distribution and severity of existing impediments to safe navigation and resource protection. RWMS information and analyses result in regional-scale permitting to accommodate water-dependent uses while minimizing environmental impacts and reducing public expenditures. Compared with traditional approaches to waterway management, the science-based RWMS is relatively unbiased, objective, transparent, ecologically sound, and fiscally prudent.