Results are reported from a 3-year monitoring initiative (2010-2013) of stable water isotopes (δ18O and δ2H) at over 50 hydrometric sites in the lower portion of the Nelson River Basin, a key freshwater-marine corridor in Canada with global significance. Data are collected from annual synoptic surveys and a time-series monitoring program. Water isotope signals exhibit significant long-term average (with reported standard deviation) differences between the upper Nelson River (-10.5‰ δ18O ± 0.18‰) and Burntwood River (i.e. Churchill Basin; -12.8‰ δ18O ± 0.4‰) regions which are attributed to the geographic extent and origin of the water. Upper Nelson River flow-isotope signals suggest a more temperate climate, and exhibit reverse seasonal cycling (i.e. ice-on isotope enrichment; ice-off isotope depletion) due to the connectivity with and influence of Lake Winnipeg. In contrast, the Burntwood River behaves like a snowmelt-dominated river heavily influenced by wetland storage and enrichment during ice-off periods, exhibiting isotopic signals negatively correlated with headwater river discharge. Flow-weighted δ18O and δ2H show decreased variability in both regions at extreme low- and high-flow regimes, indicating a tendency towards a single dominant end member: wetland release (low-flow regime) or snowmelt/rainfall (high-flow regime). Mid- to normal-flow regimes exhibit increased isotopic variability, as do small headwater catchments resulting from varied source water contributions, residence times, mixing patterns and the role of landscape-specific features. The Stable Water Isotope Monitoring Network (SWIMN) presented enables the closure of water-isotope mass balance modelling that will facilitate the understanding of changes to freshwater-marine linkages.