Peatlands have the capacity to sequester large quantities of carbon and can therefore play an important role in climate change mitigation. However, anthropogenic activities alter their hydrological regimes, converting them from net CO 2 sinks into net sources. In England and elsewhere, lowland peatlands have been heavily drained and modified for agricultural land use, resulting in some of the most productive farmland in the UK. Estimates of CO 2 emissions and water use from the area are scarce, but these data are required to understand the consequences of maintaining agricultural output whilst simultaneously reducing GHG emissions. In this paper, we compiled a uniquely comprehensive dataset of CO 2 and H 2 O flux measurements from flux towers on cropped lowland peat, and coupled this with crop calorific values to estimate carbon and water use intensities of food production on peat. Our results showed that croplands on peat emitted 23.1 ± 10.4 ton CO 2 ha −1 y −1 (mean ± SD). Sites with peat depth > 40 cm emitted 25.1 ± 9.2 ton CO 2 ha −1 , while wasted peat sites emitted 11.8 ± 4.8 ton CO 2 ha −1 . Effective water table depth and organic carbon content were the main drivers of variation in annual net ecosystem production and ecosystem respiration across sites; crop type partly followed these gradients, so may not be a direct driver of variations in emissions. ET was less variable across site‐years and depended on the phenology of crop production. When considering CO 2 emissions and water use per calorie produced, lettuce and celery rotations were the most C and water use intensive crops, with values an order of magnitude larger than cereal crops. Overall, this paper highlights the scale of CO 2 emissions from managed peatlands and the importance of balancing GHG emissions and water use with ongoing food production from these economically important areas.