Past and ongoing investigations have established that lakes in the Mackenzie River Delta collectively represent gradients in water transparency, nutrient regime, and biotic communities, each strongly linked to the sill elevations of the lakes. Analysis of 40 years of water levels in East Channel of the central delta, in combination with a floodplain geometry model to estimate river water volumes added to lake waters at the annual flood peak, permitted direct estimation of annual river-to-lake connection times, lake water renewal, and interannual variabilities in nine lakes spanning the full range of sill elevations in the delta. Results have revealed a broad range of river-to-lake connectivities and river water renewals that are temporally dynamic and vary considerably among the lakes of this river delta system. Lakes with short and variable connection times plus low and variable river water renewal yield groups of lakes with high degrees of individuality because they are strongly influenced by particular sequences of antecedent years (legacy effects) that may result in lakes simultaneously containing residual waters from multiple river inundation events separated by more than a decade. Lakes with long and less varying connection times plus high river water renewal with multiple possible river water resets per year yield lakes with high degrees of similarity. The full combination of lakes arranged in an intermittently connected continuum, creating variable connectivity for aquatic organisms and water intermixing, may be an important mechanism driving the collectively distinctive habitat productivity and biodiversity of aquatic communities in this system, relative to lakes on the surrounding landscape.