Alternate furrow fertigation has shown potential to improve water and fertilizer application efficiency in irrigated areas. The combination of simulation and optimization approaches permits to identify optimum design and management practices in furrow fertigation, resulting in optimum cost, irrigation performance or environmental impact. The objective of this paper is to apply 1D surface and 2D subsurface simulation-optimization models to the minimization of nitrate losses in two types of alternate furrow fertigation: a) variable alternate furrow irrigation; and b) fixed alternate furrow irrigation. For comparison purposes, optimizations are also reported for conventional furrow irrigation. The model uses numerical surface fertigation and soil water models to simulate water flow and nitrate transport in the soil surface and subsurface, respectively. A genetic algorithm is used to solve the optimization problem. Four decision variables (inflow discharge, cutoff time, start time and duration of fertilizer solution injection) were optimized to minimize the selected objective function (nitrate loss) for two fertigation events performed during a maize growing season. The simulation-optimization model succeeded in substantially reducing the value of the objective function, as compared to the field conditions for all irrigation treatments. In the experimental conditions, optimization led to decreased inflow discharge and fertilizer injection during the first half of the irrigation event. This was due to the high potential of the field experiment to lose water and nitrate via runoff. In the optimum conditions, alternate furrow fertigation strongly reduced water and nitrate losses compared to conventional furrow irrigation. The simulation-optimization model stands as a valuable tool for the alleviation of the environmental impact of furrow irrigation.