Imazapyr is a herbicide that can be used in irrigation canals to control a range of aquatic weed species, however, its residual nature, combined with its phytotoxicity to crops at low concentrations, means that the water in canals must be carefully managed following imazapyr application. Residues of the herbicide imazapyr (isopropylamine salt) in irrigation water were analysed and modelled after application to irrigation canals in south-eastern Australia. A treatment program to control delta arrowhead (sagittaria; Sagittaria platyphylla (Engelm.) J.G. Sm.) in over 400 km of irrigation canals was enacted by applying imazapyr to dewatered canals during winter. Following imazapyr application, canals were left dewatered for a period (up to eight weeks) and then refilled. After refilling, canals were ponded for a period (up to 28 days) to allow degradation of imazapyr in the water via photolysis. Upon refilling canals, ~650 water samples containing imazapyr were collected across the treatment area and data modelled to measure the extent of water contamination and to guide efforts to reduce the subsequent irrigation hazard to crops. Modelled data demonstrates that imazapyr behaviour in irrigation water following canal refilling was predictable when 1) amount of imazapyr applied, 2) the dewatered period following herbicide application, 3) the water ponding period, and 4) solar exposure during water ponding were taken into account. Minimising the amount applied (g imazapyr per km of canal) and maximising the time between spraying and refilling (dewatered period) reduced the initial concentration in the water following canal refilling. The amount of imazapyr in the canal water following refilling was reduced by half for every 16 days (confidence interval = 10–38 days) that the canal remained dewatered after imazapyr application. Imazapyr dissipation during the ponding period following canal refilling occurred at a rate that depended on solar exposure. Dissipation did not occur when solar exposure was <8.5 MJ m−2. However, when solar exposure was >10 MJ m−2, imazapyr concentration in the water reduced by half for every 4.4 days of ponding period (confidence interval = 2.9–9.5 days). Our two models, combined with local climate data on solar exposure, can be used by canal managers to determine the optimal time to refill canals so that imazapyr dissipation is maximised, and thus risk of damaging irrigated crops is minimised.