Biodiversity indicators are used to inform decisions and measure progress toward global targets, such as the United Nations Sustainable Development Goals. Indicators aggregate and simplify complex information, so underlying information influencing its reliability and interpretation (e.g., variability in data and uncertainty in indicator values) can be lost. Communicating uncertainty is necessary to ensure robust decisions and limit misinterpretations of trends, yet variability and uncertainty are rarely quantified in biodiversity indicators. We developed a guide to representing uncertainty and variability in biodiversity indicators. We considered the key purposes of biodiversity indicators and commonly used methods for representing uncertainty (standard error, bootstrap resampling, and jackknife resampling) and variability (quantiles, standard deviation, median absolute deviation, and mean absolute deviation) with intervals. Using 3 high‐profile biodiversity indicators (Red List Index, Living Planet Index, and Ocean Health Index), we tested the use, suitability, and interpretation of each interval method based on the formulation and data types underpinning the indicators. The methods revealed vastly different information; indicator formula and data distribution affected the suitability of each interval method. Because the data underpinning each indicator were not normally distributed, methods relying on normality or symmetrical spread were unsuitable. Quantiles, bootstrapping, and jackknifing provided useful information about the underlying variability and uncertainty. We built a decision tree to inform selection of the appropriate interval method to represent uncertainty or variation in biodiversity indicators, depending on data type and objectives. Our guide supports transparent and effective communication of biodiversity indicator trends to facilitate accurate interpretation by decision makers.