Clear Lake is a large, shallow, hypereutrophic lake in Northern California, USA. Clear Lake is an important water resource for the surrounding community offering many cultural and recreational opportunities and provides drinking water for more than half of the region's population. Despite these many ecosystem services, Clear Lake suffers from Harmful Algal Blooms (HABs) of cyanobacteria. This project aims to understand the lake and watershed processes contributing to the negative impacts on the lake water quality and ecosystem health with a goal of rehabilitating the lake. The UC Davis Tahoe Environmental Research Center conducted a 5-year (2019-2023) water quality monitoring program collecting monitoring data to better understand the physical, chemical, and biological processes affecting lake quality. Data from this monitoring program are publicly available here (DOI of EDI data repository to be provided when available). This project is funded by the California Department of Fish and Wildlife through California State Assembly Bill 707 (2017), the California Natural Resources Agency, and the UC Davis Tahoe Environmental Research Center.In addition to this overarching project, we completed additional biological and optical measurements over a shorter 1.5-year time period (Jul 2021 - Oct 2022) with the goal of supporting Phytoplankton Community Composition (PCC) and Cyanobacteria genera differentiation algorithm development from remotely sensed hyperspectral measurements. Three of these sampling events were completed coincident to whole-lake hyperspectral images collected by the DESIS sensor. These additional data included High-Performance Liquid Chromatography (HPLC) phytoplankton pigment data and above-water spectroradiometry (SVC HR-1024i) measurements. This additional work was supported by a NASA Office of STEM Engagement (OSE) graduate student fellowship awarded to Samantha Sharp in 2020 (Grant Number 80NSSC20K1458).

Field data for vertical water quality profiles using Yellow Spring Instruments (YSI) EXO2 sondes during daylight hours in Clear Lake, Lake County, California. This data release includes all measured environmental parameters included in the analysis. First release: April 13, 2019 Revised: October 29, 2019 (version. 2.0) Revised - January 24, 2022 (version 3.0) Revised - May 31, 2024 (version 4.0)

Field data for vertical water quality profiles using Yellow Spring Instruments (YSI) EXO2 sondes during daylight hours in Clear Lake, Lake County, California. This data release includes all measured environmental parameters included in the analysis. First release: April 13, 2019 Revised: October 29, 2019 (version. 2.0) Revised - January 24, 2022 (version 3.0) Revised - May 31, 2024 (version 4.0)

Field data for vertical water quality profiles using Yellow Spring Instruments (YSI) EXO2 sondes during daylight hours in Clear Lake, Lake County, California. This data release includes all measured environmental parameters included in the analysis. First posted: April 23, 2019 Revised: November 2021

The dataset provided here contains the added pixel quality assurance (QA) flags that help ensure validity of satellite-derived water quality estimates in freshwater lakes and reservoirs. This work builds upon a study by Urquhart et al. [1] where inland lake and waterbody satellite data was processed and flagged for California, Ohio, and Florida. Added pixel QA flags include land-adjacent pixels, unresolvable waterbody pixels, and snow/ice pixels. Any water pixel adjacent to land is flagged to caution potential for mixed land-water pixels and land adjacency effects. A weekly QA flag mask is provided for snow/ice presence over lakes. The unresolvable QA flag mask contains inland waterbodies smaller than 27 hectares and/or with less than three 300m resolvable satellite pixels. An updated version of the Shuttle Radar Topography Mission (SRTM) Waterbody Data (SWBD) is provided to fix a land-waterbody mask error identified in Rhode Island and Massachusetts. The Research Environments MEaSUREs SRTM, used in the NASA data pre-processing, includes the Water Body Data Shapefiles (~30m) product. Version 3.0 of the SRTM contains the vectorized coastline masks used by National Geospatial-Intelligence Agency (NGA) in the editing, called the SRTM Waterbody Data, in shapefile and rasterized formats [4]. Version 4.0 of the SRTM presented here fixes the land-waterbody mask error identified in Rhode Island and Massachusetts. Version 4.0 of the SRTM has been adopted into the NASA pre-processing of the MERIS and OLCI satellite datafiles described above. This dataset is associated with the following publication: Urquhart, E., and B. Schaeffer. Envisat MERIS and Sentinel-3 OLCI satellite lake biophysical water quality flag dataset for the contiguous United States. Data in Brief. Elsevier B.V., Amsterdam, NETHERLANDS, 28: 104826, (2020).

The dataset provided here contains the added pixel quality assurance (QA) flags that help ensure validity of satellite-derived water quality estimates in freshwater lakes and reservoirs. This work builds upon a study by Urquhart et al. [1] where inland lake and waterbody satellite data was processed and flagged for California, Ohio, and Florida. Added pixel QA flags include land-adjacent pixels, unresolvable waterbody pixels, and snow/ice pixels. Any water pixel adjacent to land is flagged to caution potential for mixed land-water pixels and land adjacency effects. A weekly QA flag mask is provided for snow/ice presence over lakes. The unresolvable QA flag mask contains inland waterbodies smaller than 27 hectares and/or with less than three 300m resolvable satellite pixels. An updated version of the Shuttle Radar Topography Mission (SRTM) Waterbody Data (SWBD) is provided to fix a land-waterbody mask error identified in Rhode Island and Massachusetts. The Research Environments MEaSUREs SRTM, used in the NASA data pre-processing, includes the Water Body Data Shapefiles (~30m) product. Version 3.0 of the SRTM contains the vectorized coastline masks used by National Geospatial-Intelligence Agency (NGA) in the editing, called the SRTM Waterbody Data, in shapefile and rasterized formats [4]. Version 4.0 of the SRTM presented here fixes the land-waterbody mask error identified in Rhode Island and Massachusetts. Version 4.0 of the SRTM has been adopted into the NASA pre-processing of the MERIS and OLCI satellite datafiles described above. This dataset is associated with the following publication: Urquhart, E., and B. Schaeffer. Envisat MERIS and Sentinel-3 OLCI satellite lake biophysical water quality flag dataset for the contiguous United States. Data in Brief. Elsevier B.V., Amsterdam, NETHERLANDS, 28: 104826, (2020).

Measurements taken in Lake Michigan and Green Bay in 2012 as part of a water quality monitoring program.

Clear Lake, located within the Coast Range west of California's Central Valley, is the largest natural freshwater lake contained fully within the state. The lake has three arms: a large open-water region to the northwest (Upper Arm), a smaller and narrower region to the southeast (Lower Arm), and the smallest and narrowest region to the east (Oaks Arm). Water quality in Clear Lake is degraded by both by mercury contamination and harmful algal blooms (HABs). The mercury contamination is largely associated with the Sulfur Bank Mercury Mine (SBMM), a Superfund site managed by the U.S. Environmental Protection Agency (USEPA) since 1992 located on the eastern end of the Oaks Arm. Mercury contamination from SBMM and its biogeochemical mercury cycling within the lake are the focus of research being conducted by the U.S. Geological Survey (USGS) in cooperation with USEPA. Monitoring and modeling efforts are being implemented to improve understanding of the ways that nutrient dynamics affect the cycling, transport, and bioaccumulation of Hg. This data release documents measurements related to organic matter concentrations and characteristics in Clear Lake, California. Data files reported here provide full spectral results for absorbance (Clear_Lake_Full_Spectra_Absorbance_Data.csv) and fluorescence (Clear_Lake_Vectorized_Fluorescence_Data.csv) analyses as well as calculated fluorescence indices and arrays (Clear_Lake_Sample_Summary.csv) used for statistical modeling for proxy development. Commonly reported diagnostic absorbance wavelengths and fluorescence excitation-emission pairs contained in these spectra as well as a set of commonly calculated indices have been released to the USGS National Water Information System (NWIS) database. The optical measurements reported here were collected to establish additional potential surrogates for mercury (Hg) and methylmercury (MeHg) concentrations and to provide more complete spectral information on temporal and spatial patterns of organic matter within the lake. Other water-quality data for the samples included in this data release are published in Marvin-DiPasquale and others (2020) and Agee and others (2024).