Fauna passages are increasingly constructed at major roads and railways to mitigate the negative effects of infrastructure and traffic on wildlife. The function of such passages depends on their design, including the construction materials, soil and vegetation. Providing 'naturalness' in fauna passages may entail significant costs, yet its benefits are incompletely understood. In particular, there is a demand for better knowledge support regarding combining passages for large fauna with minor roads, trails and watercourses. By using camera trap data collected across the passages, we examined ungulate substrate selection in seven passages serving both fauna and local roads (overpasses) and fauna and watercourses (underpasses) in boreal Sweden and Finland. While all substrates were used, during snow-free periods, ungulates used smoother surfaces (fine-grained topsoil, grass, artificial fiber mat, and dirt road) more than expected based on their availability. Coarser surface (stony/rocky ground), shrub, and water were used less than expected. The results for road and water were however inconsistent between passages; in one overpass road was instead used less than expected, and in one underpass the water section was used particularly during winter (ice cover) but also by moose wading or swimming through in summer and autumn. The general patterns of use largely remained when we analysed data on species level, although these analyses were restricted because of limited sample sizes. While our study has several limitations, it offers valuable insights for the planning and construction of fauna passages. To our knowledge, this study was the first of its kind to study the substrate preferences of ungulates in fauna passages, and we suggest to conduct further research in the field.