Abstract Geodiversity, i.e. the variety of the abiotic environment, is considered to be positively correlated to biodiversity. In streams, the importance of physical heterogeneity for biodiversity variation is well known, but the usefulness of explicitly measured geodiversity indices to account for biodiversity has not been tested. We developed a technique to measure in-stream geodiversity, based on different types of stream flow, geomorphological processes and landforms observed from photographs taken during the field work, and substrates based on traditional field observations. We further tested the utility of these geodiversity measures in explaining variation in the biodiversity of macroinvertebrates in near-pristine streams. Our specific objective was to examine the explanatory power of geodiversity compared to traditional environmental variables, such as water chemistry, depth and current velocity. While most biodiversity indices correlated more strongly with traditional environmental variables, the influence of geodiversity on biodiversity was also evident. Unique effect of flow richness on species richness and that of total geodiversity on functional richness were higher than those of the traditional environmental variables. Our findings suggested that in-stream geodiversity offers a valuable concept for characterizing stream habitats. If further developed and tested, in-stream geodiversity can be used as a cost-efficient proxy to explain variation in biodiversity in stream environments.