The lower Irwell/upper Manchester Ship Canal is a canalized waterway in the north-west of England with a catchment area of 700 km2. A 12 month study established a baseline of key chemical and physical parameters (dissolved oxygen, biological oxygen demand, temperature, pH, conductivity, NO3-, NO2-, PO43-, NH4+, suspended solids) with which episodic deteriorations in water quality along the river could be compared. The relative importance of changes in flow, and the impact of the tributaries on water quality in the Irwell, was assessed by mass balance calculations and multivariant analysis. Particular attention has been given to the interactions between sediments and the chemistry of the water column. The main conclusions to emerge are that: (i) the lower Irwell/Ship Canal is subject to significant organic pollution from storm water overflows discharging directly to the river above the study area and via its major tributaries, the Irk and Medlock; (ii) the Irk and, to a lesser extent, the Medlock have an adverse effect on water quality in the Irwell increases in mass flux below the confluences above that attributable to direct loading suggest that sediment interactions with the water column are partly responsible; (iii) high flow per se, rather than combined sewer overflows in storm events, may be causing deteriorations in water quality due to the release of pollutants from resuspended sediments; and (iv) limited storm data appear to show a readily-soluble 'first flush' of pollution to be followed by a delayed impact caused by degradation of newly introduced material. The feasibility of short-term restorative measures such as the installation of oxygen/air injection systems and the provision of weirs are examined in the context of river management; weirs do not appear to be promising solutions.