Charlotte Harbor is America's 17th largest and Florida's second largest open water estuary. It has a broad barrier island chain, large parts of which are in public ownership; its mangrove shoreline is largely intact and in public management. Regardless, the Charlotte Harbor Watershed is under significant development pressure with potential impact on storm water run-off characteristics, salinity patterns and temporal variations within the harbor, and nutrient and turbidity levels. The Harbor itself is particularly vulnerable to future degradation and therefore needs significant and sustained investment in water resource restoration. The USGS, in cooperation with South Florida Water Management District (SFWMD), performed a bathymetric survey of the lower portion of Charlotte Harbor, Pine Island Sound, and offshore of Little Gaspiralla Island to Captiva Island using a single beam hydrographic system. High resolution, acoustic bathymetric surveying is a proven method to map ocean and bay floor elevations. This report serves as an archive of processed single-beam bathymetry data that were collected in Charlotte Harbor and offshore Sanibel Island, Florida in 2003-2004. Geographic information system data products include a XYZ data, bathymetric contours, and USGS quadrangle map. Additional files include formal Federal Geographic Data Committee (FGDC) metadata.