Urban rivers worldwide are affected directly by macrophyte growth, causing reduced flow velocity and risks of flooding. Therefore, cutting macrophytes is a common management practice to ensure free drainage. The impacts of macrophyte removal on transient storage dynamics and microbial metabolic activity of wastewater-fed urban streams are unknown, preventing any assessment of the hydrodynamic and biogeochemical consequences of this management practice. Slug tracer injections were performed with the conservative tracer uranine and the reactive tracer resazurin to quantify the implications of macrophyte cutting on stream flow dynamics and metabolism. Macrophyte cutting reduced mean tracer arrival times in managed stream reaches but did not significantly decrease whole-stream microbial metabolic activity. In fact, transient storage indices were found to have increased after cutting, suggesting that macrophyte removal and the resulting increase in flow velocity may have enhanced hyporheic exchange flow through streambed sediments. Our results evidence that macrophyte cutting in nutrient-rich urban streams does not necessarily lead to lower in-stream storage and metabolism but that the gain in hyporheic exchange and streambed microbial metabolic activity can compensate for reduced in-stream storage. Increased stream flow resulting from macrophyte removal may therefore even enhance nutrient and pollutant attenuation capacity of streambed sediments.