The efficiency of nitrogen (N) use in dairy herds is an important challenge due to the environmental impacts of the N cascade and to the cost of protein resources. The assessment of global N efficiency and N excretion of dairy herds is complex due to the large diversity of feeding management during the year (several diets and several feeding groups). CowNex is a new web application (http://www.cownex-record.inra.fr/) (Project RedNex UE FP7 KBB-2007-1) that facilitates the calculation of dry matter and nitrogen use in dairy herd according to the management, with a special attention to feeding management. It is a subpart of the whole farm MELODIE model using the Record modelling platform. It simulates the daily intake, production and excretion of the different categories of animal in a dairy herd according to the feeding management described by the users. CowNex enables the assessment of existing farms and the simulations of changes in feeding management both on production and excretion. Applied to a large diversity of dairy systems encountered in France, CowNex was used to estimate the actual situation and to test some mitigation options to reduce NH3 emissions and associated N2O emissions from manure. The estimation of these impact was calculated using the EMEP-EEA equations with the CowNex results. The reduction of protein supplementation to reach a crude protein content of 14% with maize silage based diets is a simple and efficient solution to highly reduce ammonia emissions and decrease GHG emissions between 10 and 20%, with a good choice of protein sources, but without changing any manure management options. In many systems, there is both economic and environmental benefit to pay attention to the protein supplementation.