After the spread of H5N1 highly pathogenic avian influenza virus (AIV) from Asia into Russia, the Middle East, Europe, and Africa in 2005–06, the Swiss national AIV surveillance program was extended. One of the new focal points was Lake Constance, where sentinel duck stations and swim-in traps were established within the project Constanze in collaboration with Germany and Austria. More than 2000 samples from 41 species were collected in Switzerland between September 2006 and December 2008. Approximately 4% were AIV-positive by quantitative reverse transcriptase–PCR. Subsequent typing revealed 13 different AIV subtypes, of which H5N2 and H9N2 were the most prevalent. All H7 isolates and all but one H5 isolate were characterized as low pathogenic; however, a highly pathogenic H5N1 AIV was detected in a healthy pochard. This study demonstrates that a wide selection of different AIV subtypes can cocirculate among the waterfowl population in wild bird habitats.