Use of nitrogen and phosphorus in agriculture increases agricultural production but also generates important environmental problems around the world, such as high nitrate levels in aquifers and an increase in eutrophication of waters.A set of tools and models are used, ENVIRO-GRO and PATRICAL models, to analyse the effect of large irrigation system modernization, 13,700 ha, from traditional flood irrigation to modernized drip irrigation, in the aquifer nitrate levels and in the phosphorus inputs to a 50-years eutrophicated RAMSAR lake, Albufera lake.Based on data collected from end users, modernized irrigation system reduces the amount of nitrogen applied from 25 % to 45 % and phosphorus applied around 90–95 %, so phosphorus content on soil, phosphorus legacy, is reducing by time. Obtained results indicate that nitrogen leaching as nitrate is reduced by 70 % to 83 % and surface runoff during irrigation events disappear, hence phosphorus contributions to surface waters are eliminated. Nitrate polluted aquifer will be recovered in 5–6 years after complete implement of measures and phosphorus inputs to the lake are reduced around 20 % contributing to improve the status of the eutrophicated Albufera lake.Results show great agreement with the European Strategy to reduce the use of fertilizers and how the fertilizers technical management in fertigation can contribute to greater efficiency in it use and improvement of the environment.