Riparian landscapes are characterized by heterogeneous geomorphological structures such as erosive and depositional habitats, and therefore, may have variable soil biophysical properties. The heterogeneity in geomorphological structures and related biophysical properties would exert spatial variations in the soil CO2 efflux (SCE). However, studies assessing the relative control of biophysical variables on the SCE under such complex landscapes of dry tropical ecosystems are limited. Therefore, we assessed the effect of heterogeneity in geomorphological structures on SCE, and identified the key biophysical variables governing SCE along the riparian landscapes. The SCE, soil organic C (SOC), microbial biomass C (MBC) and pH were found to vary significantly (P < 0.05) along riparian habitats, and SCE was found 73% higher at erosive than depositional habitats. SOC was found as a prominent regulator of SCE which alone explained about 80% of the variability in SCE. Moreover, soil moisture, fine particles, pH and MBC also showed strong control on SCE along riparian landscapes. Stepwise regression analysis revealed that after excluding SOC as a main variable, soil moisture explained 32% of the variability in SCE at overall landscape level whereas fine particles and MBC explained 78% and 23% of the variability in SCE at erosive and depositional habitats, respectively. Overall, results indicate that erosive habitats are the major source of SCE, and variation in biophysical variables is greatly affecting the SCE at these habitats. Therefore, further assessment of interactions of SCE, soil biophysical parameters and their regulatory components such as hydrology, vegetation and anthropogenic activities at micro—(site and land-use) as well as macro—(landscape) scales would help to understand the soil C dynamics along the heterogeneous riparian landscapes under climate change scenarios. © 2019, Springer Nature Switzerland AG.