**1. Introduction**

More than half of the United States population inhabits coastal and estuarine areas [1]. These regions are under pressure as rapid population growth, overutilization of natural resources, and removal of such resources as agriculture and urban development become more predominant. Although this growth and development provide economic opportunity, they also alter local ecosystems by changing land use and land cover; causing changes in soil and groundwater chemistry, watershed-level hydrology, and dissolved nutrients in waterways, particularly in the form of nitrogen and phosphorous species [2]. According to Nehrling [3], throughout the United States, commercial fertilizer use has experienced nearly a threefold increase, from approximately 6.8 million metric tons in 1960 to about 20.0 million metric tons in 2011 in order to accommodate rapid population growth and need for increased food quantities.

According to the National Oceanic and Atmospheric Administration (NOAA) National Ocean Service [4], estuaries have been seriously impacted by various anthropogenic activities and disturbances, and many are seriously degraded by pollution. Toxic substances such as chemicals and heavy metals, nutrient pollution (resulting in eutrophication), and pathogenic bacteria and viruses are the pollutants having the greatest impact on the health of estuarine waters [4]. Estuaries by their nature are transitional areas between the land and the sea including both freshwater and saltwater environments and have the accumulative impacts of both land and water activities. By far, large-scale changes from draining, filling, damming, or dredging are the greatest threats to estuaries [4]. These activities result in immediate destruction, loss of estuarine habitats, or irreversible changes in the environment.

Given the increasing number of water quality issues such as harmful algal blooms (HABs) in economically significant waters of the world, methods are needed for early detection of these issues and their sources, which when used with other environmental and historic data can alert authorities a threatening condition. Remote sensing (RS) has the potential to provide accurate synoptic views of water quality conditions over a large spatial extent and can be used to estimate turbidity and algal biomass, and have the potential to identify algal taxonomic groups. Detection of water quality issues such as dominant algal taxonomic groups can provide coastal managers with information regarding those blooms that are potentially composed of harmful algae. As such, remote sensing is an important component of overall water quality and HAB-monitoring strategy. However, coastal and estuarine waters are optically complex and the monitoring of HABs is limited in these environments by remote sensing [5].

Major issues facing wetland habitats include long-term changes in land cover and land use (generally including agricultural activities, habitat destruction, encroachment, and historic diking of estuarine habitat) [6], shoreline hardening, shoreline erosion, and shoreline alterations anthropogenically induced to change the structure and function of the actual marsh surface such as hydrology, marsh topography, plant community, nutrient retention, tidal flooding, detritus accumulation, and availability to secondary producers [7–11].

Land-use activities by humans cause considerable changes in the magnitude and nature of many biological, chemical, and geological (-physical) constituents that are delivered and mixed in coastal water in the Mid-Atlantic Estuaries. Consequently, monitoring intensities of changes in the estuaries and bays' water properties is important to understand the propagation and modification of terrestrial components coming from the land and also their effect on coastal environments in response to catastrophic events and climate change. However, the distributions of the biogeochemical constituents of water remain poorly understood due to limited spatial and temporal sampling. Hyperspectral remote sensing provides a continuous spectrum of radiance (or reflectance) values associated with each pixel of an acquired image to capture a unique spectral signature of water quality indicators including salinity, chlorophyll-*a* (Chl-*a*), turbidity (Secchi depth), total suspended solids (TSSs), and dissolved organic materials ((DOMs)…etc.) which act as proxies for biogeochemical exchange in various coastal waters. This type of monitoring can help to understand and quantify relationships in the spatial and temporal structure of coupled physical-biogeochemical processes for the Mid-Atlantic Estuaries ecosystems.

Remote-sensing technology can also be used as a tool to help monitor the impact of invasive species in coastal areas although this is a difficult and complex task. Ozbay et al. [12] discussed how *Phragmites australis*, the common reed, has been widespread in tidal marshes of the eastern coast of the United States in the last 50 years [13, 14] and how their abilities to supplant other wetland vegetation and decrease wetland biodiversity has attracted considerable research attention in the United States. As stated by the authors, about 10–15% of Delaware's coastal wetlands are now estimated to be invaded with tall, dense stands of *P. australis* [15, 16].
