Submerged aquatic plant populations in the Susquehanna Flats of the Chesapeake Bay were followed for 18 years. An exotic species, eurasian water milfoil, Myriophyllum spicatum, increased dramatically from 1958 to 1962; at the same time the dominant native species declined. After 1962, milfoil populations declined and the native rooted aquatics gradually began to return to their former levels. In the late 1960's all species declined and in 1972 almost disappeared from the Susquehanna Flats. These fluctuations may have been related to several interrelated environmental factors in the Chesapeake Bay, including tropical storms, turbidity, salinity and disease. The utilization of the Susquehanna Flats by waterfowl appears to be related to the abundance and species composition of the submerged macrophytes present.