1. Introduction

Currently there are numerous efforts underway to improve the understanding of physical, chemical and biological characteristics of waters including remote sensing techniques. Remotely sensed data give information on the interaction between solar radiation, sea water and the different substances contained within it. Remote sensing methods can be used to determine water quality parameters, such as the trophic state, Secchi depth, turbidity, concentration of chlorophyll-a or suspended inorganic matter. The study area—Hudson/Raritan Estuary is one of the most productive regions in the world and it is declared as a major natural and scenic resource to both NY and NJ. At the same time, it is one of the most intensively developed and industrialized estuaries in the world. With increasingly sophisticated sensors, better data, and improved algorithms, water quality parameters–phytoplankton detection and species identification can be accurately determined. Remote sensing as a monitoring/management tool can complement the local and state government efforts in combating the factors attributed to water pollution control infrastructure.