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Effective environmental assessment and management requires quantifiable biodiversity targets. Biodiversity benchmarks define these targets by focusing on specific biodiversity metrics, such as species richness. However, setting fixed targets can be challenging because many biodiversity metrics are highly variable, both spatially and temporally. We present a multivariate, hierarchical Bayesian method to estimate biodiversity benchmarks based on the species richness and cover of native terrestrial vegetation growth forms. This approach uses existing data to quantify the empirical distributions of species richness and cover within growth forms, and we use the upper quantiles of these distributions to estimate contemporary, "best-on-offer" biodiversity benchmarks. Importantly, we allow benchmarks to differ among vegetation types, regions, and seasons, and with changes in recent rainfall. We apply our method to data collected over 30 yr at similar to 35,000 floristic plots in southeastern Australia. Our estimated benchmarks were broadly consistent with existing expert-elicited benchmarks, available for a small subset of vegetation types. However, in comparison with expert-elicited benchmarks, our data-driven approach is transparent, repeatable, and updatable; accommodates important spatial and temporal variation; aligns modeled benchmarks directly with field data and the concept of best-on-offer benchmarks; and, where many benchmarks are required, is likely to be more efficient. Our approach is general and could be used broadly to estimate biodiversity targets from existing data in highly variable environments, which is especially relevant given rapid changes in global environmental conditions.