Our study examined the phytoplankton component of water column reflectance at and in the vicinity of three National Estuarine Research Reserves (Apalachicola Bay, Sapelo Island, and ACE Basin). Close-range water reflectance and optically active water constituents were measured with a dual-headed Ocean Optics USB2000 system at stations selected to capture longitudinal gradients in coastal rivers and embayments. The stations included a wide range of algal, total seston, and CDOM concentrations. In October, 2002 and June, 2003, an airborne imaging spectrometer (AISA system) was flown at Apalachicola and ACE Basin, respectively, coincident with the close range measures. The close range data were used to parameterize and compare several chlorophyll prediction algorithms developed for turbid, Case II waters. These algorithms rely primarily on pigment absorption and particle scattering features in the red and lower NIR wavelengths. In turn, these algorithms were applied to pixel classifications of the imaging spectrometry data to produce chlorophyll distribution maps. Our findings have relevance to monitoring efforts and HAB detection in the optically complex coastal environments of the Southeastern U.S.