Living benthic foraminifera of Flensburg Fjord were surveyed in June 2006. The muddy and organic-rich sediments of the inner fjord were dominated by Elphidium incertum. E. incertum and E. excavatum were frequent in muds and sandy muds of the fjord loop around Holnis Peninsula and in the outer part. Gelting Bay yielded a different biofacies, indicating a brackish and sandy habitat, poor in food supply and with microfauna dominated by Ammonia beccarii and E. albiumbilicatum. The central fjord and nearshore zones of the loop were characterized by sandy muds, relatively poor in food and occupied by A. beccarii, E. incertum and E. excavatum subspecies. High abundances of E. excavatum were encountered in the innermost fjord, with fine-grained and organic-rich muddy sediments.
A comparison with previous studies revealed the profound changes in species composition in the outer Flensburg Fjord since the 1970s. A decline in numbers of Ammotium cassis and flourishing of Ammonia beccarii in Gelting Bay were recognized. These changes are most likely associated with decreased intensity and frequency of salt-water inflows into the Baltic Sea since the 1960s. It is inferred that the decline of A. cassis is similar to that of Eggerelloides scaber, which currently is found only in depressions of Kiel Bight with higher salinity.