In 2001 and 2002, fluxes of N 2O, CH 4, CO 2 and N 2 were measured in two constructed wetlands (CW) for domestic wastewater treatment in Estonia. The difference between the median values of N 2O, CH 4, and N 2 fluxes in the horizontal subsurface flow (HSSF) CWs was non-significant, being 1.3–1.4 and 1.4–4.1 mg m − 2 d − 1 for N 2O–N and CH 4–C, and 0.16–0.17 g N m − 2 d − 1 for N 2–N respectively. The CO 2–C flux was significantly lower (0.6 g C m − 2 d − 1 ) in one of the HSSF filters of a hybrid CW, whereas the single HSSF and VSSF filters emitted 1.7 and 2.0 g C m − 2 d − 1 . The median value of CH 4–C emission in CWs varied from 1.4 to 42.6 g C m − 2 d − 1 , being significantly higher in the VSSF filter beds. We also estimated C and N budgets in one of the HSSF CWs (312.5 m 2) for 2001 and 2002. The total C input into this system was similar in 2001 and 2002, 772 and 719 kg C year − 1 , but was differently distributed between constituent fluxes. In 2001, the main input flux was soil and microbial accumulation (663 kg C year − 1 or 85.8% of total C input), followed by plant net primary production (NPP) (10.2%) and wastewater inflow (3.9%). In 2002, 55.7% of annual C input was bound in plant NPP, whereas the increase in soil C formed 28.5% and wastewater inflow 15.7%. The main C output flux was soil respiration, including microbial respiration from soil and litter, and the respiration of roots and rhizomes. It formed 120 (97.5%) and 230 kg C year − 1 (98.2%) in 2001 and 2002 respectively. The measured CH 4–C flux remained below 0.1% of total C output. The HSSF CW was generally found to be a strong C sink, and its annual C sequestration was 649 and 484 kg C year − 1 per wetland in 2001 and 2002 respectively. However, negative soil and microbial accumulation values in recent years indicate decreasing C sequestration. The average annual N removal from the system was 38–59 kg N year − 1 (46–48% of the initial total N loading). The most important flux of the N budget was N 2–N emission (22.7 kg in 2001 and 15.2 kg in 2002), followed by plant belowground assimilation (2.3 and 11.9 kg N year − 1 in 2001 and 2002), and above-ground assimilation (1.9 and 9.2 kg N year − 1 , respectively). N 2O emission was low: 0.37–0.60 kg N year − 1 .