The objective of this study was to determine the long-term effects of ambient unionized ammonia nitrogen (NH3-N) combined with different feeding regimes on Atlantic salmon Salmo salar L parr growth, welfare and smoltification. Previous studies on the parr stage of Atlantic salmon have mostly focused on acute exposure, or at low temperatures. Atlantic salmon parr were exposed for 105 days (at 12°C, pH 6.8) to four sublethal ammonia concentrations ranging from 0.1 to 35 μg L−1 NH3-N (0.1–25 mg L−1 TAN) at two feeding levels: full feed strength (+20% overfeeding) and 1/3 of full feed strength. After 21 days, it was observed that 32 μg L−1 NH3-N reduced growth rate of parr fed full ration, but this effect was not evident at the end of the exposure. Feed utilization was not affected by ammonia exposure at any sampling point. Increasing ammonia levels were associated with a higher prevalence and severity of gill damage at 22 days but not at the end of the exposure. The examination of welfare indicators revealed only a few pathologies, not related to ammonia exposure. In addition, higher ammonia concentrations did not appear to influence the development of hypo-osmoregulatory ability during parr-smolt transformation.