New Zealand’s agricultural sector faces the challenge of maintaining productivity while minimizing impacts on freshwaters. This study evaluates the cost-effectiveness of various green infrastructure systems designed to reduce diffuse agricultural sediment and nutrient loads. Utilizing a quantitative economic and contaminant reduction modeling approach, we analyze the impacts of five interceptive mitigation systems: riparian grass filter strips, constructed wetlands, woodchip bioreactors, filamentous algal nutrient scrubbers, and detainment bunds. Our approach incorporates Monte Carlo simulations to address uncertainties in costs and performance, integrating hydrological flow paths and contaminant transport dynamics. Mitigation systems are assessed individually and in combination, using a greedy cyclical coordinate descent algorithm to find the optimal combination and scale of a system for a particular landscape. Applying the model to a typical flat pastoral dairy farming landscape, no single system can effectively address all contaminants. However, strategic combinations can align with specific freshwater management goals. In our illustrative catchment, the mean cost to remove the full anthropogenic load is NZD 1195/ha for total nitrogen, NZD 168 for total phosphorus, and NZD 134 for suspended solids, but results will vary considerably for other landscapes. This study underscores the importance of tailored deployment of green infrastructure to enhance water quality and support sustainable agricultural practices.