The protection of water quality in lakes, rivers, seas, oceans and coastal areas is an issue of great importance for preserving ecosystems and human health. The water quality and quantity is vital for sustainable water resources development and management. From the remote sensing perspective, waters can generally be divided in two classes: case-I and case-II waters. The formers are those dominated by phytoplankton (such as open oceans) and the latter are those containing not only phytoplankton, but also suspended sediments, dissolved organic matter and anthropogenic substances (such as coastal and inland waters).
Hyperspectral data can provide useful information to assess water quality conditions of many water aquatic ecosystems. This includes classifying the trophic status of lakes and estuaries, characterizing algal blooms and assessming ammonia dynamics for wetland treatments, predicting total ammonia concentrations by means of the hyperspectral signatures of macrophytes, determining the total suspended matter, chlorophyll content and total phosphorus. The chlorophyll, in particular, is an indicator of the algae contents and hence water quality. As regards the detection of blue-green and green algae, whose peak reflectance are close together and barely distinguishable, hyperspectral imagers provide the big advantage of being capable to improve the detection of chlorophyll, and hence algae, thanks to the narrow spectral bands that can be acquired.
PRISMA will offer the environmental managers and monitoring agencies a great opportunity for the observation of coastal, inland and estuarine waters at spatial and temporal scales not possible with traditional field measurements or ocean colour satellites. Moreover, these products could potentially help in situ sampling planning, indicating the spatial extent of an event observed in images. Some results show the potential advantage of PRISMA's full spectra data and high spatial resolution for studying complex coastal and inland waters. For example, suspended sediment concentrations are important for monitoring coastal discharge, river plume extent and resuspension events; Colored Dissolved Organic Matter serves as a nutrient source and a vector for heavy metals in water from land. Chl-a is used as a proxy for phytoplankton biomass and the other pigments (Phycocyanin, Phycoerythrin, etc.) can indicate the presence of potential harmful algal bloom.
Taking into account the high potentialities of a hyperspectral imager, the contribution of PRISMA mission in the field of water resources falls within the following applications:
· Detection, monitor and classification of pollutants on sea surfaces (oil spill, heavy metals)
· Bathymetry applications
· Chlorophyll analysis
· Analysis of optically active parameters
· Extraction of environment health-related parameters (e.g. seagrass beds and lake macrophyte)
· Detection of toxic blooming (e.g. cyanobacteria)
· Detection of suspended matter
· Measurement of photosynthetic potential by classification of different phytoplankton species
· Investigations of water quality
· Monitoring coastal erosion
· Flood detection and monitoring
 Application of hyperspectral remotely sensed data for water quality monitoring: accuracy and limitation. A.M. Bhatti, J. Schalles, D. Rundquist, L. Ramirez, S. Nasu. Accuracy 2010 Symposium, July 20-23, Leicester, UK
 A review of hyperspectral remote sensing and its application in vegetation and water resource studies. M. Govender, K. Chetty, H. Bulcock. Water SA Vol. 33 No. 2 April 2007