A total of 1991 environmental samples of fresh avian feces and urine from several aquatic bird species in a coastal area of Northeast Germany were examined for the presence of avian influenza viruses (AIV). By real-time reverse-transcriptase polymerase chain reaction, specific for an M gene of influenza A viruses, none of 659 duck samples and only 11 (0.9%) of 1,268 geese and swan samples tested positive. Two of these were identified as H5N2 viruses of low pathogenic-ity. Conventional cloacal and oropharyngeal swab samples (n=1,402) collected in an adjacent coastal region in Northeast Germany from comparable species of captured or hunted birds, yielded a similar detection rate (3/901; 0.4%) for AIV-specific RNA in geese and swans, but a higher rate (4/309; 1%) for ducks. No virus isolates were obtained from either set of samples. Collection of environmental avian samples was simple and cost effective and also allowed us to regulate sample sizes over time. A species assignment of these samples was possible, provided that close presampling observation of birds at the sampling sites was secured. Environmental sampling to monitor AIV in wild bird populations may be a valid alternative to the more-invasive and capture-dependent methods based on cloacal sampling.