waterquality for ArcGIS Pro Toolbox : user's guide

Monitoring water quality of small inland lakes and reservoirs is a critical component of the US Army Corps of Engineers (USACE) water quality management plans. However, limited resources for traditional field-based monitoring of numerous lakes and reservoirs covering vast geographic areas often leads to reactional responses to harmful algal bloom (HAB) outbreaks. Satellite remote sensing methodologies using HAB indicators is a good low-cost option to traditional methods and has been proven to maximize and complement current field-based approaches while providing a synoptic view of water quality (Beck et al. 2016; Beck et al. 2017; Beck et al. 2019; Johansen et al. 2019; Mishra et al. 2019; Stumpf and Tomlinson 2007; Wang et al. 2020; Xu et al. 2019; Reif 2011). To assist USACE water quality management, we developed an Environmental Systems Research Institute (ESRI) ArcGIS Pro desktop software toolbox (waterquality for ArcGIS Pro) founded on the design and research established in the waterquality R software package (Johansen et al. 2019; Johansen 2020). The toolbox enables the detection, monitoring, and quantification of HAB indicators (chlorophyll-a, phycocyanin, and turbidity) using Sentinel-2 satellite imagery. Four tools are available: (1) automating the download of Sentinel-2 Level-2A imagery, (2) creating stacked image with options for cloud and non-water features masks, (3) applying water quality algorithms to generate relative estimations of one to three water quality parameters (chlorophyll-a, phycocyanin, and turbidity), and (4) creating linear regression graphs and statistics comparing in situ data (from field-based water sampling) to relative estimation data. This document serves as a user’s guide for the waterquality for ArcGIS Pro toolbox and includes instructions on toolbox installation and descriptions of each tool’s inputs, outputs, and troubleshooting guidance.