Water quality monitoring is invaluable to ensure compliance with regulations, detect trends or patterns, and advance ecological understanding. However, monitoring typically measures only a few characteristics in a small fraction of a large and complex system, and thus the information contained in monitoring data depends upon which features of the ecosystem are actually captured by the measurements. Difficulties arise when these data contain something other than intended, but this can be minimized if the purpose of the sampling is clear, and the sampling design, measurements, and data interpretations are all compatible with this purpose. The monitoring program and data interpretation must also be properly matched to the structure and functioning of the system. Obtaining this match is sometimes an iterative process that demands a close link between research and monitoring.