Ecosystem function is a foundational part of ecosystem health, but it is often neglected in the practice of ecosystem management. We conducted a review of freshwater ecosystem management grey literature, analysing sixty (n = 60) documents across multiple countries and organisations to understand the prevalence of function in measures and conceptions of ecosystem health. Only 28% of analysed documents included definitions of waterway health that included function, and only 30% integrated function into their conceptions of waterway health. More generally, we observed noticeable deviation in analysed documents from management best practices advocated for by contemporary ecosystem science – including occluded rationales, vague language, and imprecise metrics for assessing waterway health. Our findings support previous observations of a strong structural bias in current ecosystem health monitoring and suggest the need for closer examinations into the processes and rationales by which such an important factor could be ignored in current monitoring programmes. We discuss these findings in broader ecosystem management contexts suggest a framework to assist practitioners in deciding when and how to incorporate measures of ecosystem function into waterway monitoring and assessment programs.