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Increase in nutrient loading into large riverine systems is of interest because of long-lasting negative effects on downstream water bodies. We know little of this phenomenon with respect to long-term relationships between water quality metrics and trends in river flow. Here we present a multi-decadal examination of nutrient transport patterns of the South Saskatchewan and Red Deer Rivers, Canada. Using a multimethod approach, we show a slightly increasing trend in annual volume of water reaching a mid-watershed reservoir (Lake Diefenbaker) concomitant with a change in seasonal variability of flow events from the 1970s. Both total nitrogen (TN) and total phosphorus (TP) flux increased during the period of record. TN concentration increased, while TP concentration decreased. On average, the high-flow season transported 95% of annual TP flux, 75% of annual TN flux, and 65% of annual flow. Inter-annually, high-flow season contributions decreased with respect to water volume, but increased with respect to both TN and TP flux. We believe that changes in variability but also timing of hydroclimatic forces are responsible for observed patterns. Higher flows and more precipitation during the high-flow season are most likely responsible for increasing nutrient load regardless of overall decreases in nutrient concentration.