The residual signals of the physical and chemical processes undergone in a river basin are stored in the isotopic composition of river water and are used here to isolate and quantify fluxes of water, energy and carbon for a large boreal river basin. The integrated nature of the river signal is exploited to provide meaningful basin-wide annual averages for fluxes difficult to quantify and extrapolate by studying highly variable interface exchanges at discrete locations. The slope of the linear regression of deuterium (δD) and oxygen (δ18O) isotopes for the Ottawa River is ∼6.0, considerably less than the slope of the local meteoric water line (7.7). This discrepancy is a consequence of evaporative loss from open water bodies and soils and, through a new method, is calculated to be 8.1% of annual precipitation. As well, on the basis of thirty years of daily meteorological and discharge data, annual evapotranspiration for the Ottawa River basin is calculated to be 53.1%. Combining the evaporation and evapotranspiration calculations apportions 45% of the water losses to transpiration. The energy required to drive these cycles is calculated to be 8% of annual solar radiation for total evapotranspiration and 13% of growing season solar radiation for transpiration. These energies are transformed into latent heat. The water use efficiency ratio is used to estimate total fixation of carbon (gross primary production (GPP)) for the basin at 15.6 mol C m−2 yr−1. This rate is substantially greater than the export of carbon via rivers plus rates estimated for carbon respiration in the literature, indicating that the boreal forest is a plausible component of the postulated “missing” carbon sink. Comparison of accumulation rates of C in peatlands and the rates required to account for the missing sink suggest that peat accumulation rates are ∼20 times too slow to account for the missing sink flux. Speculatively, the living biomass of the boreal forest is the dominant sink. Accepting this, the respiration rate needed for a steady state balance between the calculated boreal forest GPP and the missing global carbon sink is found to be around 5.6 mol C m−2 yr−1.