The Estero Bay watershed is under significant development pressure with potential impacts on storm water runoff characteristics, and changes in salinity patterns, nutrient and turbidity levels. Environmental quality in the bay is particularly vulnerable to future degradation due to increasing urbanization and the Bay's limited volume. In recent years, the Caloosahatchee Estuary system has also been impacted due to development and water management activities. These impacts have prompted the development of Minimum Flows and Levels (MFLs) for the Caloosahatchee River by the South Florida Water Management District (SFWMD). A District revision of the MFLs for the Caloosahatchee River and Estero Bay regions required the development of hydrodynamic and water quality models. The U.S. Geological Survey (USGS), in cooperation with SFWMD, performed a bathymetric survey of lower Estero Bay using single-beam and aircraft-based lidar systems. High resolution, acoustic and lidar bathymetric surveying are proven methods to map sea and river floor elevations. Survey track-lines were spaced 250-meters apart orientated along long axis of the river, bays, and estuaries. Several perimeter survey lines were also collected. This report serves as an archive of processed lidar bathymetry data that were collected in Estero Bay, Florida in 2003. Geographic Information System (GIS) data products include XYZ data, bathymetric contours, and a USGS quadrangle map. Additional files include formal Federal Geographic Data Committee (FGDC) metadata.