This study investigated carbon (CH4, CO2) and nitrogen (N2O) gaseous fluxes as finger prints for microbial wastewater treatment processes in vertical (VF) and horizontal (HF) subsurface flow mesocosms, planted with Cyperus papyrus and operated under batch hydraulic loading. The closed chamber method was used to measure gaseous emissions for 12 weeks (April–June 2014) in Kampala, Uganda. Organic matter (OM) (BOD5 and COD) and inorganic nitrogen (NH4+ and NO3−) nutrient concentrations were monitored to estimate OM degradation rates and potential nitrification and denitrification. The highest mean CH4 flux (mg CH4C m−2 h−1) was 38.3 ± 3.3 in unplanted HF compared to the lowest (3.3 ± 0.4) established in planted VF mesocosms. CO2 fluxes (mg CO2C m−2 h−1) were significantly higher (P < 0.05) in planted mesocosms, with no significant difference (P > 0.05) between the planted HF (2213.5 ± 122.4) and VF (2272.8 ± 191.0) mesocosms. The high CO2 flux was attributed to efficient degradation of the inflow organic carbon facilitated by sufficient oxygen supply especially in the planted mesocosms. Although N2O flux was relatively higher in HF mesocosms, it did not vary significantly (P > 0.05) in all treatments. Generally the results indicated significant nitrification, especially in the planted mesocosms. However, high fluxes of N2O comparable to other denitrifying CWs suggested potential for coupled nitrification and denitrification in these systems. Overall, compared to CH4 and N2O, CO2 was found to be the most significant gaseous flux under induced aerobic conditions enhanced by use of C. papyrus plants and an intermittent loading regime.