Increasing demand for global food production is leading to greater use of irrigation to supplement rainfall and enable more intensive use of land. Minimizing adverse impacts of this intensification on surface water and groundwater resources is of critical importance for the achievement of sustainable land use. In this paper we examine the linkages between irrigation runoff and resulting changes in quality of receiving surface waters and groundwaters in Australia and New Zealand. Case studies are used to illustrate impacts under different irrigation techniques (notably flood and sprinkler systems) and land uses, particularly where irrigation has led to intensification of land use. For flood irrigation, changes in surface water contaminant concentrations are directly influenced by the amount of runoff, and the intensity and kind of land use. Mitigation for flood irrigation is best achieved by optimizing irrigation efficiency. For sprinkler irrigation, leaching to groundwater is the main transport path for contaminants, notably nitrate. Mitigation measures for sprinkler irrigation should take into account irrigation efficiency and the proximity of intensive land uses to sensitive waters. Relating contaminant concentrations in receiving groundwaters to their dominant causes is often complicated by uncertainty about the subsurface flow paths and the possible pollutant sources, viz. drainage from irrigated land. This highlights the need for identification of the patterns and dynamics of surface and subsurface waters to identify such sources of contaminants and minimize their impacts on the receiving environments.