ABSTRACT Arctic freshwaters are being rapidly altered by global climate change with consequences to hydrology, biogeochemistry, and ecology, but in many cases the trajectory of these changes is poorly understood. We collected a unique 5-year time series of major ion, nutrient, and trace metal data from lakes in the Mackenzie Delta (NT, Canada) to examine limnological changes during a period of variable flood conditions, including years of recent historic high and low peak river levels. Previous work in the Mackenzie Delta has established that lake water chemistry is strongly related to connection time with the river during the period of spring ice-jam flooding or via channel connections through the growing season. We show that differences in peak spring water levels explain differences in lake chemistry in lakes isolated from the channel during the summer. Isolated, macrophyte-rich lakes in the Mackenzie Delta have been shown to be CO2 absorbers during summer. We demonstrate a response to alterations in flood regime by variables related to macrophyte productivity in isolated lakes with the greatest connectivity to the river that suggests productivity declines with increasing connection time. The connectivity of low-elevation lakes, which represent a majority of lake number and area in the Mackenzie Delta, has been projected to increase with climate change. Our work suggests that an increase in connection time may decrease the macrophyte productivity of these lakes, with potential consequences to the CO2 balance of individual lakes and the Mackenzie Delta as a whole.