Two species of the genus Ammonia, Ammonia tepida and A. aberdoveyensis, occur in the Holocene sediment successions of the former Salziger See and the Suesser See, two inland brackish-water lakes in central Germany. Thus, this work represents the first non-marine evidence of calcareous foraminifers in central Europe. A. aberdoveyensis permanently colonized the Suesser See from the early Atlantic to the Subboreal interval (∼8500–4500 cal. yr BP), whereas tests of A. tepida were found only during the Atlantic interval (∼8500–5600 cal. yr BP). Except for some redeposited specimens, the foraminiferal record of the former Salziger See is characterized by the monospecific appearance of A. tepida during the late Atlantic interval (∼6500 cal. yr BP). Both a high rate of test aberrancy of the observed Ammonia specimens and their high test porosity can be associated with enhanced environmental stress within the lake ecosystems caused by hyposalinity and/or periodically low oxygen concentration in the lake bottom waters. Because during the Quaternary, the study area has never been connected to the ocean, an airborne colonization of the Mansfeld lakes by migratory birds can be assumed. The low diversity of the investigated foraminiferal fauna is consistent with the remote position of the study area—more than 300 km from the natural habitat of foraminifers in the Baltic and North Seas—and the tolerance of the genus Ammonia to a wide range of environmental conditions.