This study analyses the spatial and temporal variability of chlorophyll-a in Chesapeake Bay; assesses the performance of Ocean Color 3M (OC3M) algorithm; and develops a novel algorithm to estimate chlorophyll-a for coastal shallow water. The OC3M algorithm yields an accurate estimate of chlorophyll-a concentration for deep ocean water (RMSE=0.016), but it failed to perform well in the coastal water system (RMSE=23.17) of Chesapeake Bay. A novel algorithm was developed which utilizes green and red bands of the Moderate Resolution Imaging Spectroradiometer (MODIS) sensor. The novel algorithm derived the chlorophyll-a concentration more accurately in Chesapeake Bay (RMSE=4.20) than the OC3M algorithm. The study indicated that the algorithm that uses red bands could improve the satellite estimation of chlorophyll-a in the coastal water system by reducing the noise associated with bottom reflectance and colored dissolved organic matter (CDOM)