Satellite remote sensing can be an effective alternative for mapping cyanobacterial scums and aquatic macrophyte distribution over large areas compared with traditional ship's site-specific samplings. However, similar optical spectra characteristics between aquatic macrophytes and cyanobacterial scums in red and near infrared (NIR) wavebands create a barrier to their discrimination when they co-occur. We developed a new cyanobacteria and macrophytes index (CMI) based on a blue, a green, and a shortwave infrared band to separate waters with cyanobacterial scums from those dominated by aquatic macrophytes, and a turbid water index (TWI) to avoid interference from high turbid waters typical of shallow lakes. Combining CMI, TWI, and the floating algae index (FAI), we used a novel classification approach to discriminate lake water, cyanobacteria blooms, submerged macrophytes, and emergent/floating macrophytes using MODIS imagery in the large shallow and eutrophic Lake Taihu (China). Thresholds for CMI, TWI, and FAI were determined by statistical analysis for a 2010-2016 MODIS Aqua time series. We validated the accuracy of our approach by in situ reflectance spectra, field investigations and high spatial resolution HJ-CCD data. The overall classification accuracy was 86% in total, and the user's accuracy was 88%, 79%, 85%, and 93% for submerged macrophytes, emergent/floating macrophytes, cyanobacterial scums and lake water, respectively. The estimated aquatic macrophyte distributions gave consistent results with that based on HJ-CCD data. This new approach allows for the coincident determination of the distributions of cyanobacteria blooms and aquatic macrophytes in eutrophic shallow lakes. We also discuss the utility of the approach with respect to masking clouds, black waters, and atmospheric effects, and its mixed-pixel effects.

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