Meandering through the most densely populated metropolitan areas of Taipei, Taiwan, the Danshui River and its tributaries have undergone the construction of 14 wetlands since 2004, as a means to improve water quality. This study was conducted to examine the functional capabilities associated with treating non-point source pollution through these riparian wetlands. Trend analysis was used to differentiate dissolved oxygen, biochemical oxygen demand, suspended solids, ammonia, and Escherichia coli, among 13 sampling sites using both functions of a Mann–Kendall test and a seasonal Mann–Kendall test. The results show that water quality in Taipei metropolitan rivers has been improving since increasing the number of constructed wetlands and connecting households to the public sewage system. The concentration of pollutants such as those influencing biochemical oxygen demand have gradually declined in drought seasons because riparian wetlands contribute a base flow to dilute riverine pollutants. This paper indicates that the creation of treatment systems influences dissolved oxygen conditions at the municipal scale, suggesting that constructed wetlands could stabilize water quality during extreme hydrological events and improve water quality particularly in times of drought.