Indicators are increasingly used to measure environmental systems; however, they are often criticized for failing to measure and describe uncertainty. Uncertainty is particularly difficult to evaluate and communicate in the case of composite indicators which aggregate many indicators of ecosystem condition. One of the ongoing goals of the Ocean Health Index (OHI) has been to improve our approach to dealing with missing data, which is a major source of uncertainty. Here we: (1) quantify the potential influence of gapfilled data on index scores from the 2015 global OHI assessment; (2) develop effective methods of tracking, quantifying, and communicating this information; and (3) provide general guidance for implementing gapfilling procedures for existing and emerging indicators, including regional OHI assessments. For the overall OHI global index score, the percent contribution of gapfilled data was relatively small (18.5%); however, it varied substantially among regions and goals. In general, smaller territorial jurisdictions and the food provision and tourism and recreation goals required the most gapfilling. We found the best approach for managing gapfilled data was to mirror the general framework used to organize, calculate, and communicate the Index data and scores. Quantifying gapfilling provides a measure of the reliability of the scores for different regions and components of an indicator. Importantly, this information highlights the importance of the underlying datasets used to calculate composite indicators and can inform and incentivize future data collection.