The aim of this study is to compare methane (CH4) and nitrous oxide (N2O) fluxes from horizontal subsurface flow (HSSF) and vertical subsurface flow (VF) systems treating municipal wastewater in tropical climates. The treatment performance from both systems was monitored simultaneously with CH4 and N2O fluxes to observe the relationships between them. Average CH4 fluxes of 5.4 mg·m−2·h−1 and 9.5 mg·m−2·h−1, and N2O fluxes of 0.32 and 0.21 mg·m−2·h−1 were measured from VF and HSSF systems, respectively. The average CH4 fluxes measured during the wet period were 63.5% and 44% less than those recorded during the dry period for HSSF and VF systems, respectively; those for N2O fluxes were 47% and 38% less than the dry period for these systems, respectively. The CH4 and N2O fluxes from both HSSF and VF dropped as a result of rainfall events and slowly increased after days with no rainfall. Influent total organic carbon (TOC) and total nitrogen (TN) concentrations are found to be the dominant factors regulating the fluxes where significant correlations between CH4 and N2O with the influent TOC and TN concentrations were found in both systems.