Little is understood on the interaction between irrigated agriculture and surface water quality in South African catchments. A case study was conducted on the Middle Olifants Catchment, which contains the second largest irrigation scheme in South Africa. Dams, rivers, irrigation canals, and drainage canals were sampled between the Loskop and Flag Boshielo Dams. Results were compared to historical water quality monitoring data from the Department of Water and Sanitation (DWS). While DWS data indicate that phosphate-phosphorus (PO4-P) does not pose a eutrophication risk, our monitored data were above the eutrophication threshold for the majority of the sampling period. In general, phosphorus (P) pollution is a bigger issue than nitrogen (N), and concentrations of these nutrients tend to be higher during the summer rainfall months, potentially indicating a link to agriculture and fertilization events. We estimated that waste water treatment works (WWTW), which are currently systematically failing in South Africa, have the potential to pollute as much P as irrigated agriculture. Electrical conductivity levels increased downstream, moving from the acceptable towards the tolerable category, while the sodium adsorption ratio (SAR) presents a moderate risk of infiltrability problems. The pH values were generally in the ideal range. This study has highlighted existing and looming water quality issues for irrigation and the environment in the Middle Olifants. Similar scoping studies are recommended for other intensively-irrigated catchments in the region to identify issues and allow timely intervention.