Nitrogen dynamics were studied over 3 years in pilot-scale surface flow constructed wetlands (SFCWs) treating three strengths of ammonium-rich swine wastewater. A high removal rate of ammonium (1.2–2.9 g m−2 d−1) and total nitrogen (1.5–3.5 g m−2 d−1) was achieved from highstrength wastewater in the SFCWs. Nitrate concentration was significantly higher (p < 0.01) in the effluent than in the influent, and the increased nitrate concentration did not significantly affect ammonium removal in the SFCWs. The effluent nitrate concentration showed annual cyclical changes and could be described using a harmonic regression equation over time (y = a + b sin (2π/365.25 t + c); R2 = 0.152–0.566). The multiple regression equation (R2 = 0.200–0.551) indicated that water temperature and oxidation reduction potential were the primary factors affecting nitrate accumulation in the SFCWs. The abundance of nitrification functional genes (amoA in ammonia-oxidizing archaea and bacteria) was higher in spring and winter than in summer. The abundance of denitrification functional genes (narG, nirK, nirS, and nosZ) was higher in summer than in spring and winter. At cold temperatures (5–10 °C), nitrate accumulated significantly in the water column rather than in the sediments and the potential nitrification rates increased slightly, suggesting the importance of nitrogen transformation in the water column during nitrogen removal. These results are helpful for selecting targeted seasonal intensification strategies to improve the SFCWs performance.