This paper examines the spatial patterns of optically active constituents and the basis for chlorophyll estimation algorithms in optically complex (Case 2) versus less complex, phytoplankton dominated (Case 1) waters. The challenges of Case 2 water optics have stimulated significant advancements in bio-optical modeling and insights into the interactions of optical constituents. Chlorophyll is a comparatively efficient and effective, albeit indirect, measure of phytoplankton biomass and is widely used in assessments of coastal and inland waters. Most approaches for remote estimation of phytoplankton chlorophyll are based on the absorption of water column sunlight by algal pigments in the presence of light scattering by algal cells and non-algal particles. This interplay of pigment-specific absorption and particle scattering produces graded responses in the emergent reflectance spectra signals detectable by radiometer instruments. Coastal, estuarine, and inland water habitats present serious challenges to the interpretation of diagnostic light signals because of the diversity of optically active constituents, which partially mask the fundamental phytoplankton absorption and scattering relationships. Since 1997, we measured hyperspectral water reflectance, chlorophyll, suspended solids, and CDOM in the estuarine mixing zones and near shore waters of 15 rivers in five states between Mississippi and Delaware and will extend this work in Chesapeake Bay in July, 2005. Chlorophyll concentrations varied over three orders of magnitude (0.2 to about 400 mg/m3), yet followed orderly patterns within mixing zone transects. We will compare different schemes (semi-empirical and inverse modeling) for optimum efficiency and accuracy in remote chlorophyll assessments in Case 2 waters.