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The size and distribution of Phytoplankton populations are indicators of the ecological status of a water body. The chlorophyll-a (Chl-a) concentration is estimated as a proxy for the distribution of phytoplankton biomass. Remote sensing is the only practical method for the synoptic assessment of Chl-a at large spatial and temporal scales. Long-term records of ocean color data from the MODIS Aqua Sensor have proven inadequate to assess Chl-a due to the lack of a robust ocean color algorithm. Chl-a estimation in shallow and coastal water bodies has been a challenge and existing operational algorithms are only suitable for deeper water bodies. In this study, the Ocean Color 3M (OC3M) derived Chl-a concentrations were compared with observed data to assess the performance of the OC3M algorithm. Subsequently, a regression analysis between in situ Chl-a and remote sensing reflectance was performed to obtain a green-red band algorithm for coastal (case 2) water. The OC3M algorithm yielded an accurate estimate of Chl-a for deep ocean (case 1) water (RMSE = 0.007, r2 = 0.518, p < 0.001), but failed to perform well in the coastal (case 2) water of Chesapeake Bay (RMSE = 23.217, r2 = 0.009, p = 0.356). The algorithm developed in this study predicted Chl-a more accurately in Chesapeake Bay (RMSE = 4.924, r2 = 0.444, p < 0.001) than the OC3M algorithm. The study indicates a maximum band ratio formulation using green and red bands could improve the satellite estimation of Chl-a in coastal waters.