There are various methods for measuring flow rates in rivers, but all of them have practical issues and challenges. A period of exceptionally high water levels revealed substantial discrepancies between two measurement setups in the same waterway. Finding a causal explanation of the discrepancies was important, as the problem might have ramifications for other flow-rate measurement setups as well. Finding the causes of problems is called diagnostic problem-solving. We applied a branch-and-prune strategy, in which we worked with a hierarchy of hypotheses, and used statistical analysis as well as domain knowledge to rule out options. We were able to narrow down the potential explanations to one main suspect and an alternative explanation. Based on the analysis, we discuss the role of statistical techniques in diagnostic problem-solving and reasoning patterns that make the application of statistics powerful. The contribution to theory in statistics is not in the individual techniques but in their application and integration in a coherent sequence of studies - a reasoning strategy.