In many smallholder farming areas southern Africa, the cultivation of seasonal wetlands (dambos) represent an important adaptation to climate change. Frequent droughts and poor performance of rain-fed crops in upland fields have resulted in mounting pressure to cultivate dambos where both organic and inorganic amendments are used to sustain crop yields. Dambo cultivation potentially increases greenhouse gas (GHG) emissions. The objective of the study was to quantify the effects of applying different rates of inorganic nitrogen (N) fertilisers (60, 120, 240 kg N ha−1) as NH4NO3, organic manures (5,000, 10,000 and 15,000 kg ha−1) and a combination of both sources (integrated management) on GHG emissions in cultivated dambos planted to rape (Brassica napus). Nitrous oxide (N2O) emissions in plots with organic manures ranged from 218 to 894 µg m−2 h−1, while for inorganic N and integrated nutrient management, emissions ranged from 555 to 5,186 µg m−2 h−1 and 356–2,702 µg m−2 h−1 respectively. Cropped and fertilised dambos were weak sources of methane (CH4), with emissions ranging from −0.02 to 0.9 mg m−2 h−1, while manures and integrated management increased carbon dioxide (CO2) emissions. However, crop yields were better under integrated nutrient management. The use of inorganic fertilisers resulted in higher N2O emission per kg yield obtained (6–14 g N2O kg−1 yield), compared to 0.7–4.5 g N2O kg−1 yield and 1.6–4.6 g N2O kg−1 yield for organic manures and integrated nutrient management respectively. This suggests that the use of organic and integrated nutrient management has the potential to increase yield and reduce yield scaled N2O emissions.