Degradation of urban stream ecosystems caused as a direct result of stormwater runoff is well documented. The signs of degradation are universal and include altered hydrology, reduced stream function and significant declines in biodiversity. Within urban landscapes, concrete stormwater channels are ubiquitous. They are designed to efficiently transport stormwater runoff, which is typically achieved via the widening, deepening, straightening and concrete lining of what was once a complex stream ecosystem that performed multiple natural functions. In concrete channels the alteration of stream hydrology and physical structure are particularly stark, leading to the understandable perception that concrete channels are far more degraded than nearby urban streams. But, the validity of this perception has not been explored. Literature on the biodiversity of concrete stormwater channels is sparse and studies comparing biodiversity of urban streams to concrete stormwater channels are virtually non-existent. In this study, we set out to compare aquatic biodiversity of urban streams to that in concrete stormwater channels and minimally disturbed reference streams. We used benthic diatoms as indicators of water quality and aquatic macroinvertebrates as indicators of local in-stream habitat and catchment disturbance. Results show benthic diatom community structure varied significantly between reference streams and both urban streams and concrete channels. However, urban streams and concrete channels had similar diatom communities. Similarly, the comparison of aquatic macroinvertebrate communities revealed significant variation for comparison of reference streams to both urban streams and concrete channels, whilst there was only a slight variation in communities between urban streams and concrete channels. Results of this study imply that altered flow, not degraded water quality or loss of local in-stream habitat is the most important factor which detrimentally effects urban waterways