The lowland ponds, depressional submerged areas that are fed by runoff from surrounding uplands and then send overflows to downstream water bodies, are recognized as biogeochemical hotspots of nitrogen (N) removal. Despite their important role in mitigating N pollution, very little is currently known about their potential for N removal, particularly for those ponds draining contrasting land uses. Our study investigated the variabilities of N removal in different types of ponds from a hilly watershed by quantifying gaseous N2 emission fluxes. The mean excess N2 concentrations relative to its saturations varied within 0.41–16.44 μmol L−1, demonstrating that significant N removal occurred in all of the ponds. Further estimates of net N2 fluxes suggested that ponds impacted by different land use types exhibited distinct potentials for N removal. The ponds that drained tea plantations, which are a typical form of agriculture in hilly regions, had the highest N removal rate (6.48 mmol N2 m−2 d−1), equivalent to ~2.3, 3.0, and 5.8 times those drained by residential areas, mixed-landscape, and forests, respectively. The levels of dissolved oxygen and nutrient supply affected by the different drained land uses were responsible for the different potentials of N removal. Our results suggest that there is a need for integrated management strategies that not only focus on optimization of environmental conditions in ponds but also consider the impacts of the land use compositions in their drainages to more efficiently promote N removal.