Context This is the first research to investigate the impact of irrigation duration on crop productivity and nitrogen (N) performance indicators in southern New South Wales (SNSW), Australia, as the industry strives for improved N productivity. Aim To benchmark the impact of different irrigation durations on waterlogging and related impacts on available soil and fertiliser N, cotton productivity and nitrogen use efficiency (NUE). Methods Two field experiments were conducted in SNSW where cotton was grown with varying rates of fertiliser N application interacting with different durations of furrow irrigation applications during the period from first flower to crop maturity. Key results Waterlogged conditions occurred within the top 20 cm of the soil profile during irrigations. These conditions coincided with fertiliser placement and high concentrations of available mineral N, which created conditions conducive for N loss. However, the internal NUE (kg lint kg crop N uptake−1) and N balance were not impacted by irrigation duration in either experiment, despite differences in duration of waterlogged conditions that averaged 15 h irrigation−1. Partial N budgets suggested that 48% of the available N to the crop could not be found in the plant or soil mineral N pools after harvest. Conclusion Modification of the duration of irrigation applications was not an effective management option to improve NUE in irrigated cotton; however, it improved water productivity (bales per megalitre). Implications Further research is required to consider the implications of other irrigation systems such as overhead sprinkler and drip systems for improvement of NUE.