The Kat River is an agricultural catchment that drains salt rich geology. Potential salinity impacts on ecological condition of the river were investigated. Monthly salt concentrations and flow discharges were monitored at ten sites along the Kat River below the Kat Dam. Monthly salt loads were computed to relate salinity to land use and ionic data used to assess the toxicity of major salts using the TIMS model. Concentration duration curves for sodium chloride were derived from flow concentration relationships, representing sodium chloride concentrations to which the aquatic ecosystem had been exposed. The ecological condition was assessed at nineteen sites using SASS5 biotic index over four seasons. Finally, the modelled instream salt concentrations and bioasessments were evaluated in terms of the modelled level of species protection afforded at different salt concentrations. Species Sensitivity Distributions (SSDs) were used for this exercise. There was a general downstream increase in salinity with the minimum concentrations recorded at the Fairbain tributary (84 mg/L) and maximum levels at the sewage outfall in Fort Beaufort (1222 mg/L). There was evidence that citrus irrigation upstream of Fort Beaufort increased salinisation. Sodium chloride, and to a lesser extent magnesium sulphate, were the dominant salts in the Kat River catchment, with the latter being more toxic. However these had little or no impact on the aquatic ecosystem. Flow-derived sodium chloride concentrations showed that both the Balfour and Blinkwater tributaries were in a fair/ poor condition. However with regard to ecological condition, it was demonstrated that the river is generally in a good state except for the Blinkwater River and the lower catchment. Degraded habitat condition at the Blinkwater was responsible for poor ecological condition. Integrating SSD derived classes, sodium chloride classes and ecological condition indicated that sodium chloride is a driver of ecological condition at the sewage treatment works and the subsequent site (only two of nineteen biomonitoring sites).