This paper demonstrates the characterization of the water properties, bathymetry, and bottom type of the Indian River Lagoon (IRL) on the eastern coast of Florida using hyperspectral imagery. Images of this region were collected from an aircraft in July 2004 using the Portable Hyperspectral Imager for Low Light Spectroscopy (PHILLS). PHILLS is a Visible Near InfraRed (VNIR) spectrometer that was operated at an altitude of 3000 m providing 4 m resolution with 128 bands from 400 to 1000 nm. The IRL is a well studied water body that receives fresh water drainage from the Florida Everglades and also tidal driven flushing of ocean water through several outlets in the barrier islands. Ground truth measurements of the bathymetry of IRL were acquired from recent sonar and LIDAR bathymetry maps as well as water quality studies concurrent to the hyperspectral data collections. From these measurements, bottom types are known to include sea grass, various algae, and a gray mud with water depths less than 6 m over most of the lagoon. Suspended sediments are significant (~35 mg/m3) with chlorophyll levels less than 10 mg/m3 while the absorption due to Colored Dissolved Organic Matter (CDOM) is less than 1 m-1 at 440 nm. Hyperspectral data were atmospherically corrected using an NRL software package called Tafkaa and then subjected to a Look-Up Table (LUT) approach which matches hyperspectral data to calculated spectra with known values for bathymetry, suspended sediments, chlorophyll, CDOM, and bottom type.