This thesis applies several different remote sensing techniques to data collected from 2005 to 2007 on central Indiana reservoirs to determine the best performing algorithms in estimating the cyanobacterial pigments chlorophyll a and phycocyanin. This thesis is a set of three scientific papers either in press or review at the time this thesis is published. The first paper describes using a curve fitting model as a novel approach to estimating cyanobacterial pigments from field spectra. The second paper compares the previous method with additional methods, band ratio and semi-empirical algorithms, commonly used in remote sensing. The third paper describes using a partial least squares (PLS) method as a novel approach to estimate cyanobacterial pigments from field spectra. While the three papers had different methodologies and cannot be directly compared, the results from all three studies suggest that no type of algorithm greatly outperformed another in estimating chlorophyll a on central Indiana reservoirs. However, algorithms that account for increased complexity, such as the stepwise regression band ratio (also known as 3-band tuning), curve fitting, and PLS, were able to predict phycocyanin with greater confidence.