The results from measuring PAH and metal contamination together with macroinvertebrate communities at 62 headwater stream sites gives a significant insight into the range and scale of contamination. Monitoring streambed sediments at 62 sites from rural to inner city and in industrial locations presented a unique opportunity to distinguish the conditions that enhance pollution runoff at sites that are less obviously ‘at risk’ and to compare these results with sites of expected high contamination, for example in industrial areas and at motorway junctions. We used pCCA (partial Canonical Correspondence Analysis) to tease out the relationships between individual macroinvertebrate families and specific metal and PAH contaminants, and showed that it is not always the metals and PAHs with the greatest total concentrations that are doing the damage to the ecology. Ni and Zn are the critical metals, while benzo(b)fluoranthene, anthracene and fluoranthene are the most contaminating PAHs. The results identify previously unrecognized ‘high risk’ pollution sources, lay byes used for commercial parking, on-street residential parking areas, and the junctions at the bottom of hills with traffic lights, where surface runoff feeds rapidly to the streams. While this study looks at sites across Yorkshire, UK, it clearly has a broader significance for understanding contamination risks from diffuse runoff as a prerequisite for effective sustainable urban drainage system (SUDS) agendas and the protection of urban stream ecology.