# Nearshore Benthic Mapping in the Great Lakes:
## 1 Introduction  
Lake and ocean bottom, or benthic habitats, are critical zones of interface between the physical processes that shape lake morphology and surface geology and a large number of species that need specific bottom types for shelter, feeding, and reproduction [1]. The Laurentian Great Lakes comprise the largest assemblage of inland waterbodies in North America and are strongly influenced by biological processes associated with the lake floor, which contribute to whole-lake productivity and biodiversity [2]. Many native fishes and other aquatic species have strong associations with substrates for spawning and cover. Simultaneously, the lake bottom is increasingly dominated by benthic invasive species which have induced dramatic whole-lake phase shifts in food webs, water quality, and the fisheries economy [3]. Furthermore, impacts from anthropogenic forces (development, deforestation, shoreline armoring, wetland dewatering, etc.) have resulted in whole-lake changes, such as to chemical, physical, and biological integrity. As a result, the Great Lakes Water Quality Agreement was signed in 1972, amended in 1983 and 1987, and updated again in 2012 to help restore and protect the basin, in which ecosystem monitoring is a key objective for adaptive management, environmental policy, and decision making [4]. However, monitoring ecosystem trends over time remains a challenging task, especially over such a vast geographic, environmentally complex, and dynamic system like the Great Lakes. Specifically, progress in lake and marine coastal ecosystem restoration, monitoring, and management continues to be hindered by a lack of consistent, high-resolution mapping of nearshore substrate and associated habitat, including submerged aquatic vegetation (SAV). Historically, nearshore substrate and associated habitats have been mapped in a spatially and temporally piece-meal fashion with varying spatial resolution, coverage, and accuracy around the Great Lakes [5]. Data sources typically include discrete bottom grab samples, in situ measurements, and single- and multi-beam depth soundings, while more recent methods, such as satellite and airborne imagery and light detection and ranging (lidar) data, offer repeatable and consistent temporal and spatial coverage. Given environmental variability in the basin and limitations associated with each data collection method, no single solution works well in all areas. Thus, detailed substrate and habitat maps only exist in scattered, isolated areas where data resolution is sufficient, often supporting individual restoration project engineering and design, and the only basin-wide information describing geomorphology, substrate, and habitat is available at a broad scale [6]. Ultimately, this means that data gaps exist, leaving managers without the sufficient spatial, temporal, or data coverage detail needed to describe substrate and habitat features [5]. In order to work towards a solution to overcome these gaps, it will take a multi-data fusion approach, capitalizing on the strengths of individual data collection methods and technologies. Despite challenges with mapping nearshore benthic substrate and habitat, advancements have been made in the development and application of remote sensing technology for mapping complex coastal and inland waterbodies [7; 8]. The first of these advancements is increased spatial coverage of passive electro-optical multi- and hyperspectral imagery with increased spatial, spectral, and temporal resolutions in both airborne and spaceborne platforms. Additionally, there is increased coverage from active sensors, such as airborne lidar and spaceborne radar, in which sensors emit and measure returned light or microwave energy, respectively.