An extensive amount of literature on linkages between the in-stream physical environment and river benthic macroinvertebrates reports a number of relationships across multiple spatial scales. We analyzed data on different spatial scales to elucidate the linkages between different measurements of hydromorphological degradation and commonly used macroinvertebrate indices. A regression analysis of 1049 sites from 3 countries revealed that the strongest relationship between a biotic metric—average score per taxon—and physiochemical variables (R2 = 0.61) was obtained with a multiple regression model that included concentration of total phosphorus and percent arable land in the catchment, as well as hydromorphological quality variables. Analyses of 3 data sets from streams primarily affected by hydromorphological degradation showed an overall weak relationship (max R2 = 0.25) with the River Habitat Survey data of 28 Swedish streams, whereas moderate (R2 ≈ 0.43) relationships with more detailed measurements of morphology were found in 2 Danish studies (39 and 6 streams, respectively). Although evidence exists in the literature on the importance of physical features for in-stream biota in general and macroinvertebrates specifically, we found only relatively weak relationships between various measures of hydromorphological stress and commonly used macroinvertebrate assessment tools. We attribute this to a combination of factors, including 1) the mixed nature of pressures acting on the majority of river reaches, 2) scaling issues (spatial and temporal) when relating habitat surveys to macroinvertebrate assessments, and 3) the scope of commonly used macroinvertebrate assessment systems (mainly focusing on water chemistry perturbation, such as eutrophication and acidification). The need is urgent to develop refined and updated biological assessment systems targeting hydromorphological stress for the use of the European Water Framework Directive (WFD) and national water-related policies.