One of the main threats to freshwater resources is pollution from anthropogenic activities such as rapid urbanization and excessive agricultural nutrient runoff. Remote sensing technologies have been effectively used in monitoring and mapping rapid changes in the marine environment and assessing the overall health of freshwater ecosystems. The main goal of this study is to comparatively evaluate the performance of index-based and classification-based approaches in mapping dense floating algal blooms observed in Lake Burdur using Sentinel-2 imagery. For index-based mapping, algae-specific indices, namely the Floating Algae Index (FAI), Adjusted Floating Algae Index, Surface Algal Blooms Index (SABI), and Algal Blooms Detection Index (ABDI), were used. At the same time, pixel- and object-based Random Forest (RF), eXtreme Gradient Boosting (XGBoost), and Long Short-Term Memory Network (LSTM) were utilized for classification-based algal mapping. For this purpose, seven Sentinel-2 images, selected through time series analysis performed on the Google Earth Engine platform, were used as the primary dataset in the application. The results show that high-density floating algae formations can be detected over 99% by both indices and classification-based approaches, whereas pixel-based classification is more successful in mapping low-density algal blooms. When two-class thematic maps representing water and floating algae classes were considered, the maps produced by index-based FAI using an appropriate threshold value and the classification-based RF algorithm reached an overall accuracy of over 99%. The highest algae density in the lake was observed on July 13, 2021, and was determined to be effective in ~ 45 km2 of the lake’s surface.