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With growing global demand for food, the agriculture sector worldwide is under pressure to intensify and expand, risking acceleration of existing negative biodiversity impacts. Agriculture is the dominant source of ammonia (NH3) emissions, which can impact biodiversity directly through dry deposition as NH3 and by wet deposition following conversion to ammonium (NH4) in the atmosphere. Nitrogen deposition is one of the leading causes of global decline in biodiversity alongside changing land use and climate. Natura 2000 sites which are intended to protect important habitats and species across Europe, require strict levels of protection to ensure designated features achieve favourable conservation status. Many of these sites are nitrogen-limited, and/or contain sensitive species such as lichens or mosses. This project carried out ambient NH3 monitoring on selected Irish Natura 2000 sites, in order to establish potential impacts from agricultural NH3. Monitoring on twelve Natura 2000 sites observed concentrations ranging from 0.47 to 4.59 μg NH3 m−3, from which dry deposition was calculated to be 1.22–11.92 kg N ha−1 yr−1. European Monitoring and Evaluation Programme (EMEP) was used to quantify wet deposited NH4 and nitrogen oxides (NOx), in addition to dry deposited NOx on monitored sites. Estimated total nitrogen deposition ranged between 5.93 and 17.78 kg N ha−1 yr−1. On average across all monitored sites, deposition was comprised of 50.4%, 31.7%, 7.5%, and 10.3% dry NH3, wet NH4, dry NOx and wet NOx respectively. Implications for Irish agriculture are discussed in the light of both this monitoring and the European Commission Dutch Nitrogen Case (C 293/17 & C 294/17), highlighting a number of recommendations to aid compliance with the EU Habitats Directive (92/43/EEC).