Analysis of the color of water bodies is concerned with understanding what gives water its color (the “forward” problem), and the use of the remotely observed color to learn about “color producing agents” within the water (the “inverse” problem). Recently the study of water color has been going through a rapid expansion in sensors, coverage area, and algorithms. Similarly, the interest in the derived color-producing agents (CPA) is growing from both scientific interests and agencies in charge of monitoring water bodies; for example, for harmful algal blooms. Monitoring the color of water bodies remotely has the advantage of unparalleled coverage in space and time. However, this approach is limited by both the inability to operate when conditions are cloudy and the fact that the signal is emanating from only the surface layer of the water and from a different depth at each wavelength.