The aerobic oxidation of ammonia can be carried out through the first step of the nitrification process by a diverse assemblage of prokaryotes, namely the ammonia-oxidising bacteria, the ammonia-oxidising archaea, and the recently discovered complete ammonia oxidisers. Ammonia plays a major role in primary productivity in most aquatic systems where nitrogen is normally a limiting nutrient. In estuarine and coastal ecosystems, there is a strong gradient in many physical and chemical variables, particularly high salinity fluctuations, which may provide niche segregation for the ammonia-oxidising communities and processes. In this chapter, an overview of the current knowledge on the effect of salinity gradients in the estuarine prokaryotic communities responsible for aerobic ammonia oxidation will be presented. Here, we will focus on the niche differentiation strategies adopted by ammonia oxidisers to cope up with the coastal and estuarine salinity gradients.