In freshwater the super-labile dissolved organic carbon (DOC) drives extraordinarily high rates of bacterial respiration. Yet methods to directly measure the bacterial use of this DOC, without manipulating the water sample, have been illusive, until now. Here a simple inexpensive respiration chamber-valve system is described that was attached to an optical dissolved oxygen (DO) probe to measure in situ respiration. DO measurements for 5 min provided enough data to mathematically hind-cast the DO decay rate at the initial sampling point to estimate the super-labile DOC bacteria used as substrate for respiration. The method was validated in the freshwater of boreal, sub-tropical and tropical climatic zones. Bacterial respiration rates were as much as 25 times higher than the currently published rates in freshwater lakes. The super labile DOC estimated here would be missed in other bacterial respiration studies that remove the water sample from the water body. The results suggest that DOC inputs into freshwater ecosystems and the current global estimates of pCO2 outgassing into the atmosphere from bacterial respiration are being underestimated.