The rapid loss of biodiversity in freshwater systems asks for a robust and spatially explicit understanding of species' occurrences. As two complementing approaches, habitat suitability models provide information about species' potential occurrence, while environmental DNA (eDNA) based assessments provide indication of species' actual occurrence. Individually, both approaches are used in ecological studies to characterize biodiversity, yet they are rarely combined. Here, we integrated high-resolution habitat suitability models with eDNA-based assessments of aquatic invertebrates in riverine networks to understand their individual and combined capacity to inform on species' occurrence. We used eDNA sampling data from 172 river sites and combined the detection of taxa from three insect orders (Ephemeroptera, Plecoptera, Trichoptera; hereafter EPT) with suitable habitat predictions at a subcatchment level (2 km2). Overall, we find congruence of habitat suitability and eDNA-based detections. Yet, the models predicted suitable habitats beyond the number of detections by eDNA sampling, congruent with the suitable niche being larger than the realized niche. For local mismatches, where eDNA detected a species but the habitat was not predicted suitable, we calculated the minimal distance to upstream suitable habitat patches, indicating possible sources of eDNA signals from upstream sites subsequently being transported along the water flow. We estimated a median distance of 1.06 km (range 0.2–42 km) of DNA transport based on upstream habitat suitability, and this distance was significantly smaller than expected by null model predictions. This estimated transport distance is in the range of previously reported values and allows extrapolations of transport distances across many taxa and riverine systems. Together, the combination of eDNA and habitat suitability models allows larger scale and spatially integrative inferences about biodiversity, ultimately needed for the management and protection of biodiversity.