Microbial source tracking (MST) has become a focus of some recreational beach monitoring programs. Suspected sources of contamination include human sewage, agricultural runoff, and feces from wildlife and domestic animals, depending on beach location. Waterfowl have been suggested as a primary source of fecal contamination at many beaches, but techniques to “prove” contaminating microbes are of avian origin are mostly unsubstantiated. Researchers often rely on bird counts to measure the impact of waterfowl on beach health. Since waterfowl populations at Door County, Wisconsin (USA) beaches are transitory, this study focused on enumeration of avian waste material along beach transects, rather than on once per day “snapshot” bird counts. Escherichia coli (E. coli) concentration in beach water was not correlated with avian waste counts at the ten beaches studied in 2004 or the 13 studied in 2005 (rural to semi-urban). Bird counts correlated with E. coli concentrations in beach water at 30% of the sample sites in 2004 and at only one site in 2005. During the 2004 swimming season avian waste counts correlated with bird counts at only one beach and there was no correlation in 2005. These results indicate that neither avian waste enumeration nor bird counts can successfully be used to predict microbial contamination of recreational water at selected Great Lakes beaches.