The successful restoration and design of urban streams requires a clear understanding of the factors influencing the retention or cycling of nutrients at different scales or reaches. Here, we sought to determine the extent to which in stream physical complexity drives the patterning of biogeochemical activity (e.g., hot spots and hot moments) of sand-bed streams in urban Perth, Western Australia. This information will guide living stream design criteria to mitigate possible impacts of pollutants, including excess nutrients. We used a gridded sampling design to measure a range of environmental attributes from the water column and sediment (including nutrients, turbidity, temperature, flow rate, water isotopes) and related these to physical traits (e.g. channel width, stream depth, debris density, riffles). We compared spatial patterns across highly degraded (drain) and relatively natural urban stream reaches to investigate: (i) if the diversity of biogeochemical hotspots is greater in relatively natural reaches compared to drains, (ii) the extent to which hotspot development can be predicted by environmental variables, and (iii) the geomorphic characteristics most effective at increasing rates of nutrient retention within streams. This study presents the initial findings of a PhD project investigating the links between biogeochemistry and aquatic foodwebs of urban streams.