Globally, hydrological connectivity between rivers and their floodplains has been reduced by river flow management and land transformation. The Saskatchewan River Delta is North America’s largest inland delta and a hub for fish and fur production. To determine the influence of connectivity on limnology within this northern floodplain, water chemistry and stable isotopes (δ18O and δ2H) were analyzed during the winter of 2014 in 26 shallow lakes along a hydrological gradient. A total of five lake connectivity categories were determined by optical remote sensing imagary of surface water coverage area from years of varying flood intensities. Accuracy of categories was verified by degree of 18O and 2H enrichment within lakes. Both isotopes showed marked successional enrichment between connectivity categories, with more isolated lakes exhibiting greater enrichment. Water chemistry in lakes with greater connectivity to the main channel were characterized by higher pH, dissolved oxygen, nitrates, and sulfates and lower total nitrogen, total phosphorus, and ammonium compared with more isolated lakes. These findings illustrate how connectivity influences water chemistry in northern floodplain lakes and how it might determine the suitability of these lakes as winter refuge for fishes. Additionally, our study provides supporting evidence for the effective use of optical remote sensing imagery, an inexpensive and accessible source of data for researchers, when determining connectivity characteristics of large northern floodplain systems. Additionally, this study provides further evidence that the inundation of floodplain lakes by river water during peak discharge has an impact on the conditions within the lakes long into the winter ice-cover season. Understanding the year-round influence of river–floodplain connection is imperative for assessing potential impacts of climate change and future water regulation on such ecosystems.