Regions with intensive agriculture and high livestock populations go along with regional nitrogen (N) surpluses and losses of N mainly through ammonia (NH3) emissions. The deposition of this NH3 endangers (semi-)natural ecosystems including wetlands, which provide a variety of ecosystem services. The Follow’N’Flow project supported by SNF Sinergia investigates the entire N cascade from the livestock excreta on the farm via (short-range) transport and dispersion in the air and deposition till the impacts in a wetland ecosystem in the Canton of Lucerne. Beside monitoring the N flows on the farm, this includes measurements of NH3 emissions and of the NH3 deposition downwind of the source and into the nearby semi-natural wetland ecosystem. In the wetland, also the induced N2O emissions (so-called “indirect agricultural emissions”) and the exchange of other greenhouse gases are monitored in connection to the wetland ecosystem functioning. This is the first study in Switzerland that directly links agricultural NH3 emissions to NH3 deposition, and its effect on the environment.