Nitrogen removal processes and nitrogen mass balances in algae-based ponds (ABPs) and duckweed ( Lemna gibba)-based ponds (DBPs) were assessed during periods of 4 months, each under different operational conditions. During periods 1 and 2, the effect of cold and warm temperature was studied. During periods 2 and 3, the effect of low- and high-system organic loading (OL) was studied in warm seasons operation. The pilot-scale systems consisted of four similar ponds in series fed with domestic sewage with hydraulic retention time of 7 days in each pond. Overall nitrogen removal was higher during warm temperature in both ABPs and DBPs, but similar during periods 2 and 3. Nitrogen removal in DBPs was lower than in ABPs by 20%, 12% and 8% during cold temperature, warm temperature and high-OL periods, respectively. Depending on temperature and OL rate, ABPs showed higher nitrogen removal via sedimentation (46–245% higher) compared to DBPs. Also, ABPs also showed higher nitrogen removal via denitrification (7–37% higher) compared to DBPs. Ammonia volatilisation in both systems did not exceed 1.1% of influent total nitrogen during the entire experimental period. N uptake by duckweed corresponds to 30% of the influent nitrogen during warm/low OL period and decreased to 10% and 19% during the cold and warm/high OL period, respectively. Predictive models for nitrogen removal presented a good reflection of nitrogen fluxes on overall nitrogen balance under the prevailing experimental conditions.