Estuaries are an important link between terrestrial and marine ecosystems, so assessing their health and what influences it can help guide future ecosystem monitoring and management. But estuaries can be complex and dynamic systems, so summarising health by a single score or grade raises questions about interpretation, variability, sensitivity and confidence. Such questions may include how variable is the score for a particular waterway, how sensitive is the score to seemingly benign decisions taken to reach that score, and how different is the B grade of one waterway to the C scored by an adjacent waterway. Focusing on a specific estuarine health index, we quantified two different sources of variation in its construction and examined how they contributed to the variability of the final score. We found that quantifying the variability in two steps of the index construction enabled us to make more informed inferences about the index and its bearing on an overall report card score for an estuary. By highlighting uncertainty in an estuarine health index, we are improving its inferential value and enabling more defensible decision-making about current and future management and amelioration of an estuary’s health and function.