Aquatic biodiversity in rivers and streams is threatened in many regions worldwide. As biodiversity loss has severe consequences on ecosystem functioning, it is important to understand the causes of decline and to predict biodiversity in space and time. In order to achieve this, the identification of the driving factors and the appropriate choice of indicator groups are needed. We developed a spatially explicit habitat distribution model for aquatic macroinvertebrates in Swiss watercourse networks using national biodiversity monitoring data from 410 randomly selected sampling sites. We specifically looked at two worldwide frequently used macroinvertebrate indicator groups. Using generalized linear models, we related firstly species richness of mayfly, stonefly and caddisfly (Ephemeroptera, Plecoptera, Trichoptera; EPT) and secondly richness of all macroinvertebrate families and higher-order taxa (macroinvertebrate family richness) to 38 nationwide available environmental variables. We then predicted richness of both indicator groups at the landscape scale, providing the first nationwide prediction of EPT species and macroinvertebrate family richness. Consistent with previous work, we found that variables describing land use and topology were most important for explaining richness at the landscape level. However, the two indicator groups showed opposing patterns of richness and a different sensitivity to land-use variables. This indicates that the sole use of one of these groups may be misleading with respect to water quality assessments and to the identification of overall diversity hotspots. We conclude that commonly used richness patterns derived from aggregated groups, such as family-level macroinvertebrate richness, may be less appropriate for conservation strategies.