Fontanile is a Po Valley (Italy) quasi-natural lowland spring built in the middle age. This paper identifies options for the conservation of the Fontanile water dependent ecosystem, using scenarios and simulations, and exploring different policy options. Three modeling analysis have been performed: the first was carried out for estimating groundwater contamination and recharge from above, the second for evaluating the function of vegetative filter strip on the surface water quality and the last one for testing pesticide drift reduction due to the vegetative filter strip. Uncertainty characterization included climate change projections. Despite the nitrate concentration in water could favorite the eutrophication phenomena, this not occurs because of the low phosphate concentration in water and of the presence of arboreal shade. Therefore, the protection strategies must focus on sustaining desirable water quantity conditions. Water saving and conservation technologies that improve the agricultural productivity but reduce the Fontanile water flow and large buffer strips that have a limited efficacy due to the Fontanile hydrological settings can be judged as ecological traps. Inefficient irrigation systems, good agricultural practices, integrated pest management and arboreal filter strip can preserve the quality of those ecosystems.