Photo by John Hart–Wisconsin (Madison) State Journal
Yes, Canada geese are a problem for water quality, largely due to the incredible amount of goose pooh left on City streets, bike path, and picnic lawns, and swimming beaches. The City of Madison has taken steps to remove a large number of the non-migratory geese that inhabit the Lake Wingra watershed year round.
There are opinions on all sides of the issue. For related stories from the Wisconsin State Journal see these links.