The micro-scale spatial distribution patterns of a demersal fish and decapod crustacean assemblage were assessed in a hard-bottom kelp environment in the southern North Sea. Using quadrats along line transects, we assessed the in situ fish and crustacean abundance in relation to substratum types (rock, cobbles and large pebbles) and the density of algae. Six fish and four crustacean species were abundant, with Ctenolabrus rupestris clearly dominating the fish community and Galathea squamifera dominating the crustacean community. Differences in the substratum types had an even stronger effect on the micro-scale distribution than the density of the dominating algae species. Kelp had a negative effect on the fish abundances, with significantly lower average densities in kelp beds compared with adjacent open areas. Averaged over all of the substrata, the most attractive substratum for the fish was large pebbles. In contrast, crustaceans did not show a specific substratum affinity. The results clearly indicate that, similar to other complex systems, significant micro-scale species–habitat associations occur in northern hard-bottom environments. However, because of the frequently harsh environmental conditions, these habitats are mainly sampled from ships with sampling gear, and the resulting data cannot be used to resolve small-scale species–habitat associations. A detailed substratum classification and community assessment, often only possible using SCUBA diving, is therefore important to reach a better understanding of the functional relationships between species and their environment in northern temperate waters, knowledge that is very important with respect to the increasing environmental pressure caused by global climate change.