Testate amoebae (Protista: Amoebozoa) are a group of unicellular protozoans that occur widely in freshwater environments, moist soils and peatlands. They are sensitive to many environmental variables, including temperature, pH, substrate characteristics and hydrological parameters. Their shells (or tests) are resistant to dissolution and preserve well in sediments. Subfossil testate amoebae assemblages preserved in cores have thus been widely to infer past environmental conditions, particularly in peatlands, where they have become an important group for the study of Holocene climate change. This paper will review the utility of testate amoebae for water quality reconstruction in lakes, drawing on surficial sediment and core data from contaminated lakes in the Greater Toronto region and the UK. The group have remained relatively unexplored in lake environments, yet their excellent preservation potential, ease of preparation and analysis, and sensitivity to nutrient enrichment and other contaminants (e.g. winter de-icing salts), underlines their potential for biomonitoring and water quality assessment. Case studies that aim to better elucidate species-environment relationships and community interactions will be described, and the challenges imposed by taxonomic uncertainties for some taxa discussed.