Techniques are described for debugging a processing element (or elements) in a stream based database application in a manner that reduces the impact of debugging the processing element (or elements) on the overall running environment by selectively fusing (or un-fusing) processing elements running on a group of compute nodes. In addition to fusing and un-fusing processing elements or otherwise modifying a state of the stream application, a debugging application and stream manager may modify data flows within the application stream in a variety of ways to minimize any disruption resulting from a debugging session.