Substrate stability is a key determinant of stream invertebrate community composition, but its measurement can be problematic. Stream ecologists often use different approaches and techniques to quantify bed stability, and this variability makes comparison among studies difficult. We examined the link between 6 reach-scale measures of substrate stability and invertebrate community metrics in 12 New Zealand mountain streams. The strength of the link varied with the method used to define substrate stability. We used morphological budgeting to measure spatial patterns and volumes of scour and fill. We found that as erosion of sediments increased, invertebrate diversity declined exponentially. In particular, increases in the volume of scour reduced taxonomic richness, whereas deposition of coarse sediments was less relevant for invertebrate communities. Overall, the distance travelled by in-situ-marked tracer stones was most strongly linked with all invertebrate community metrics, whereas the bottom component of the Pfankuch Index related very well to diversity. Both metrics showed near-linear declines in diversity with decreasing stability. In contrast, the link between invertebrate communities and the proportion of bed area affected by entrainment was weak. Therefore, we propose tracer-based indices and the Pfankuch bottom component as the most suitable measures for research involving invertebrate–substrate-stability relationships. Measures derived from in-situ-marked tracer stones reflected only entrainment and transport of particles. In contrast, the bottom component of the Pfankuch Index encompassed the widest range of bed-stability characteristics but is prone to observer bias. An objective method that combines the efficiency of the Pfankuch Index with the characteristics measured using tracer stones could serve as a powerful explanatory tool in stream ecology.