Under the Fog: Examining the potential of shipboard hyperspectral sensors for monitoring water quality in San Francisco Bay

San Francisco Bay is a complex estuarine environment supporting a range of biodiversity and a large economy. As a highly dynamic system with rapidly shifting water masses, it is important that monitoring efforts evolve to provide information in real-time throughout the bay. Hyperspectral remote sensing using satellite and airborne platforms has proven to be a vital tool monitoring in the past, both for freshwater and marine systems, but has been underutilized in San Francisco Bay because of optical complexity, spatial scales, and the prevalence of dense fog. Here, we have taken advantage of a regular monitoring program by the USGS to test the functionality and ability of three shipboard hyperspectral radiometers to collect useful above-water data. The goal of this project is to evaluate these sensors in terms of their data quality, and explore what can be discerned about water quality of San Francisco Bay from hyperspectral optical data. In order to examine data quality, we conducted Signal-to-Noise and uncertainty analysis for all three sensors. To examine what can be discerned from this data we implemented several optical retrieval algorithms and compared them to in situ measurements. These included Fluorescent Line Height (FLH; proxy for chlorophyll), Suspended Particulate Matter (SPM), and a phytoplankton functional type algorithm, PHYDOTax. We found that SPM retrievals performed well, while FLH retrievals performed relatively poorly. PHYDOTax retrievals did well at stations with high marine influence, but decreased in accuracy at stations with more freshwater influence. This project provides a characterization of three sensors and a brief exploration of their capabilities, laying the groundwork for developing infrastructure for optical monitoring in San Francisco Bay.