Pollutants can be reduced, ameliorated, or assimilated when riparian ecosystems have the vegetation, water, and soil/landform needed for riparian functions. Loss of physical form and ecological function unravels assimilation processes, increasing supply and transport of pollutants. Water quality and aquatic organisms are response measures of accumulated upstream discharges, and ultimately of changes in riparian functions. Thus, water quality monitoring often fails to identify or lags behind many causes of pollution or remediation from riparian degradation. This paper reviews the interagency riparian proper functioning condition (PFC) assessment for lotic (running water) riparian ecosystems and outlines connections between PFC and water quality attributes (sediment, nutrients, temperature, and dissolved oxygen [DO]). The PFC interaction of hydrology, vegetation, and soils/landforms influences water quality by dissipating energy associated with high waterflow, thereby reducing vertical instability and lateral erosion while developing floodplains with captured sediment and nutrients. Slowing flood water enables aquifer recharge, deposition, and plant nutrient uptake. Water-loving, densely rooted streambank stabilizing vegetation and/or wood helps integrate riparian functions to maintain channel pattern, profile, and dimension with characteristics for a diversity of habitats. A complex food web helps slow the nutrient spiral with uptake and storage. Temperature fluctuations are dampened by delayed discharges, narrower and deeper active channels, coarser substrates that enhance hyporheic interchange, and shade from riparian vegetation. After assessment and implementation, monitoring recovery of impaired riparian function attributes (e.g., streambank plant species) naturally focuses on persistent drivers of water quality and aquatic habitat. This provides timely environmental indicators of stream ecological health and water quality remediation projects or land management.