A majority believe that transnational waters are more likely to spur conflict that cooperation. There are a number of examples of conflict (Israel and neighbors,* India and Pakistan, China and everyone, etc.), but most of these conflicts are "under control" through negotiations, agreements, etc.
In fact, there are very few examples of conflict OVER waters (the 1967 Six Day war, among them), and a number of examples of cooperation based on the necessity of sharing waters.
We probably pay more attention to conflicts that stick in our minds (and serve the rhetorical needs of politicians) than pragmatic "making do" cooperation.
Bottom Line: Transboundary waters can help neighbors build good relations, but populist demagogues prefer to use them to stir nationalist hatred of "others" (often for the benefit of domestic special interests).
* The Swiss recently released a report on Water and peace in the Middle East [pdf]