Both anthropogenic activities and natural factors affect river water in quantity and quality, while anthropogenic activities have been often blamed to cause water quality temporal degradation. In addition, riverine water quality displays intra-annual/seasonal variations, which are often more prominent than inter-annual variations. The intra-annual variations in water quality, which are attracting the attention of managers and policy-makers, beg the question of how to better manage riverine water quality at a finer time resolution. The natural factors, in particular, the hydro-meteorological variables, could be the primary drivers of the intra-annual variations of riverine water quality. Therefore, this paper examined the association between riverine water quality and one hydro-meteorological variable (flow) with the focus on their relationship at the intra-annual timescale on three selected rivers in Alberta, Canada. The results demonstrated that flow drives intra-annual variation of riverine water quality in general. Moreover, some water quality parameters responded to flow distinctively at three flow regimes (low, medium, and high flows). Water quality parameters were categorized into eight groups according to their responses to flow at the flow regimes. These implied the challenges in water quality management while providing insight into how to formulate more effective water management strategies.