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Bioindication, evaluating biological responses to environmental disturbances, is crucial for assessing the ecological status of an ecosystem. While historical bioindication relied on macroscopic organisms, the introduction of environmental DNA (eDNA) techniques allows the application of protists without the necessity of morphological identification. In this study, we propose a novel bioindication methodology utilizing Arcellinida, a group of top predators among protists, as bioindicators of freshwater ecosystems. For that purpose, we first characterized the Arcellinida diversity over 1 year at three different points of Lake Sanabria, an ancient glacier lake known to be subjected to anthropogenic disturbances. We compared this diversity with an undisturbed control site. Second, we characterized the Arcellinida diversity in other ecosystems to generate the ecological background to test the connectivity between them. Results indicate limited connectivity between the different ecosystems and an edge effect between terrestrial and aquatic ecosystems. Disturbed freshwater ecosystems exhibited reduced Arcellinida diversity at both specific and infraspecific levels, providing valuable insight into recent disturbances. Arcellinida‐based bioindication provides a sensitive, accurate and easy‐to‐interpret protocol for monitoring disturbances in freshwater ecosystems. It represents a valuable tool for environmental assessments and conservation strategies. [ABSTRACT FROM AUTHOR]