Satellite data provide the only viable means for extensive monitoring of remote and large freshwater systems, such as the Amazon floodplain lakes. However, an accurate atmospheric correction is required to retrieve water constituents based on surface water reflectance ( ${\mathrm{R}}_{\mathrm{W}}$ ). In this paper, we assessed three atmospheric correction methods (Second Simulation of a Satellite Signal in the Solar Spectrum (6SV), ACOLITE and Sen2Cor) applied to an image acquired by the MultiSpectral Instrument (MSI) on-board of the European Space Agency’s Sentinel-2A platform using concurrent in-situ measurements over four Amazon floodplain lakes in Brazil. In addition, we evaluated the correction of forest adjacency effects based on the linear spectral unmixing model, and performed a temporal evaluation of atmospheric constituents from Multi-Angle Implementation of Atmospheric Correction (MAIAC) products. The validation of MAIAC aerosol optical depth (AOD) indicated satisfactory retrievals over the Amazon region, with a correlation coefficient (R) of ~0.7 and 0.85 for Terra and Aqua products, respectively. The seasonal distribution of the cloud cover and AOD revealed a contrast between the first and second half of the year in the study area. Furthermore, simulation of top-of-atmosphere (TOA) reflectance showed a critical contribution of atmospheric effects (>50%) to all spectral bands, especially the deep blue (92%–96%) and blue (84%–92%) bands. The atmospheric correction results of the visible bands illustrate the limitation of the methods over dark lakes ( ${\mathrm{R}}_{\mathrm{W}}$ < 1%), and better match of the ${\mathrm{R}}_{\mathrm{W}}$ shape compared with in-situ measurements over turbid lakes, although the accuracy varied depending on the spectral bands and methods. Particularly above 705 nm, ${\mathrm{R}}_{\mathrm{W}}$ was highly affected by Amazon forest adjacency, and the proposed adjacency effect correction minimized the spectral distortions in ${\mathrm{R}}_{\mathrm{W}}$ (RMSE < 0.006). Finally, an extensive validation of the methods is required for distinct inland water types and atmospheric conditions.

Satellite remote sensing data have been used for water quality mapping, but accurate water reflectance retrieval is dependent on multiple procedures, such as atmospheric and adjacency corrections. For the latter, physical-based methods are used to minimize the adjacency effects caused by neighboring land targets close to water pixels, and implementation requires atmospheric and environmental parameters, such as aerosol optical depth and horizontal range (i.e., distance in meters) of the adjacency effect (${\mathrm{H}}_{\mathrm{Adj}}$). Generally, the ${\mathrm{H}}_{\mathrm{Adj}}$ is empirically defined by users and can lead to substantial errors in water reflectance when incorrectly used. In this research, a physical-based approach with three empirical methods to determine the ${\mathrm{H}}_{\mathrm{Adj}}$ (fixed, SIMilarity Environment Correction—SIMEC, and Adaptative Window by Proportion—AWP-Inland Water) were used to correct and characterize the adjacency effects in Sentinel-2 images over Brazilian inland waters. An interactive inversion method of the deep blue waveband estimated the aerosol loading for the atmospheric correction procedure. The results of atmospheric and adjacency corrections were validated against in-situ reflectance data. The inverted aerosol loading achieved a good agreement with in-situ measurements, especially at visible wavelengths (Mean Absolute Percentage Error—MAPE for eutrophic (~56%), bright (~80%), and dark (~288%) waters). The adjacency correction performance was near similar between the SIMEC and AWP-Inland Water methods in eutrophic and bright waters (MAPE difference < 3%). However, only the AWP-Inland Water method provided a smaller error (MAPE ~53%) for dark waters compared to the fixed (~108%) and SIMEC (~289%) methods, which shows how critical ${\mathrm{H}}_{\mathrm{Adj}}$ parametrization is for low water reflectance values. Simulations of different atmospheric and adjacency effects were performed, and they highlighted the importance of adjacency correction under aerosol loading higher 0.1, which is a typical aerosol loading in a dry climate season, and over extremely dark, low-reflectance waters. This paper contributes to further understanding adjacency effects in medium spatial resolution imagery of inland waters using a physical-based approach including the uncertainties in ${\mathrm{H}}_{\mathrm{Adj}}$ determination.

Due to increasing algae bloom occurrence and water degradation on a global scale, there is a demand for water quality monitoring systems based on remote sensing imagery. This paper describes the scientific, theoretical, and methodological background for creating a cloud-computing interface on Google Earth Engine (GEE) which allows end-users to access algae bloom related products with high spatial (30 m) and temporal (~5 day) resolution. The proposed methodology uses Sentinel-2 images corrected for atmospheric and sun-glint effects to generate an image collection of the Normalized Difference Chlorophyll-a Index (NDCI) for the entire time-series. NDCI is used to estimate both Chl-a concentration, based on a non-linear fitting model, and Trophic State Index (TSI), based on a tree-decision model classification into five classes. Once the Chl-a and TSI algorithms had been calibrated and validated they were implemented in GEE as an Earth Engine App, entitled Algae Bloom Monitoring Application (AlgaeMAp). AlgaeMAp is the first online platform built within the GEE platform that offers high spatial resolution of water quality parameters. The App benefits from the huge processing capability of GEE that allows any user with internet access to easily extract detailed spatial (30 m) and long temporal Chl-a and TSI information (from August 2015 and with images every 5 days) throughout the most important reservoirs in the State of São Paulo/Brazil. The application will be adapted to extend to other relevant areas in Latin America.