Endosulfan (6,7,8,9,10,10-hexachloro-1,5,5a,6,9,9a-hexahydro-6,9methano-2,4,3-benzodioxathiepin 3-oxide), a pesticide that is highly toxic to aquatic organisms, is widely used in the cotton (Gossypium hirsutum L.) industry in Australia and is a risk to the downstream riverine environment. We used the GLEAMS model to evaluate the effectiveness of a range of management scenarios aimed at minimizing endosulfan transport in runoff at the field scale. The field management scenarios simulated were (i) Conventional, bare soil at the beginning of the cotton season and seven irrigations per season; (ii) Improved Irrigation, irrigation amounts reduced and frequency increased to reduce runoff from excess irrigation; (iii) Dryland, no irrigation; (iv) Stubble Retained, increased soil cover created by retaining residue from the previous crop or a specially planted winter cover crop; and (v) Reduced Sprays, a fewer number of sprays. Stubble Retained was the most effective scenario for minimizing endosulfan transport because infiltration was increased and erosion reduced, and the stubble intercepted and neutralized a proportion of the applied endosulfan. Reducing excess irrigation reduced annual export rates by 80 to 90%, but transport in larger storm events was still high. Reducing the number of pesticide applications only reduced transport when three or fewer sprays were applied. We conclude that endosulfan transport from cotton farms can be minimized with a combination of field management practices that reduce excess irrigation and concentration of pesticide on the soil at any point in time; however, discharges, probably with endosulfan concentrations exceeding guideline values, will still occur in storm events.