Protozoans are unicellular, eukaryotic organisms that have typical internal structures like animal cells and perform all animal-like functions. They are essential components of aquatic ecosystems and soil biodiversity, contributing significantly to energy transfer to higher trophic levels and organic matter decomposition. They are abundantly present in a variety of environmental conditions and widely distributed, as well as being relatively sensitive to different contaminants. Protozoa are promising candidates for bioindication of water quality and soil health. The purpose of the present review was to highlight the importance of protozoa as bioindicators for water quality monitoring. The basic aim of bioindication is the use of biota as indicators of environmental conditions. Three broad categories of bioindicators can be recognized based on their aims and objectives: environmental, ecological, and biodiversity indicators. There are seven key advantages of Protista bioindicators, namely: environmental sensitivity, functional importance, distribution, size and numbers, response times, ease of analysis, and preservation potential. Concerning water pollution, protozoa seem to be an excellent tool to assess both toxicity and pollution of effluent water of treatment plants, and water quality in both freshwater and marine ecosystems.