This dataset contains rice crop biomass, and greenhouse gas flux measurements from five plots exposed to different fertiliser treatments and continuous and intermittent irrigation protocols. The gas flux data include methane, nitrous oxide, and ammonia, which were measured using chamber methodologies. The dataset also includes irrigation protocols and site environmental properties such as soil pH, bulk density, and texture. Agronomic yields are reported in terms of rice grain and total crop harvests as well as total nitrogen use efficiency. This dataset was created as part of an experiment carried out in rice paddies at the Indian Agricultural Research Institute (Delhi, India) in 2016. The experiment aimed to compare the environmental impacts of continuous and intermittent flooding of rice in relation to methane, nitrous oxide and ammonia emissions and the implications for nitrogen use efficiency and yield. Full details about this dataset can be found at https://doi.org/10.5285/46aafc00-6742-41df-b8be-09a8d5d86610
