Stream ecosystem metabolism plays a critical role in planetary biogeochemical cycling. Stream benthic habitat complexity and the available surface area for microbes relative to the free-flowing water volume are thought to be important determinants of ecosystem metabolism. Unfortunately, the engineered deepening and straightening of streams for drainage purposes could compromise stream natural services. Stream channel complexity may be quantitatively expressed with hydraulic parameters such as water transient storage, storage residence time, and water spiralling length. The temperature dependence of whole stream ecosystem respiration (ER), gross primary productivity (GPP) and net ecosystem production (NEP = GPP-ER) has recently been evaluated with a "natural experiment" in Icelandic geothermal streams along a 5-25 degrees C temperature gradient. There remained, however, a substantial amount of unexplained variability in the statistical models, which may be explained by hydraulic parameters found to be unrelated to temperature. We also specifically tested the additional and predicted synergistic effects of water transient storage and temperature on ER, using novel, more accurate, methods. Both ER and GPP were highly related to water transient storage (or water spiralling length) but not to the storage residence time. While there was an additional effect of water transient storage and temperature on ER (r(2) = 0.57; P = 0.015), GPP was more related to water transient storage than temperature. The predicted synergistic effect could not be confirmed, most likely due to data limitation. Our interpretation, based on causal statistical modelling, is that the metabolic balance of streams (NEP) was primarily determined by the temperature dependence of respiration. Further field and experimental work is required to test the predicted synergistic effect on ER. Meanwhile, since higher metabolic activities allow for higher pollutant degradation or uptake, river restoration and management should promote habitat diversity and complexity (hyporheic zone, macrophyte patches, substrate heterogeneity), especially for microbial activity.