This dataset is part of the article with DOI: https://doi.org/10.3389/fenvs.2023.1130655. In the article, the authors employed satellite-derived Water Quality Indicators and spatiotemporal analysis to assess the risk of wastewater contamination in Conceição Lagoon, a coastal lagoon in Southern Brazil. The WQIs used are satellite-derived absorption coefficients of chlorophyll-a (chla) and coloured dissolved organic matter (CDOM), and the backscattering coefficient of suspended particulate matter (SPM). The dataset comprises: 1) time series (2019-2021) of WQIs generated from the processing of Sentinel-2 Level 2A scenes with the 2SeaColor model, 2) time series (2019-2021) of the WQIs standardized anomalies (WQIs_Anomalies), and 3) time series (2019-2021) of the final Wastewater Contamination Index (WCI). The files are raster stacks in ENVI format (flat-binary raster file with an accompanying ASCII header file - *.HDR), which can be opened with most GIS software. The header file contains metadata of the rasters, including the coordinate system, pixel size, and band names (which in this case correspond to the image date in the format YYYYmmdd). More details on the methods can be found in the associated article.