This paper explores the importance of the N loss pathways relative to the immobilisation and soil mineral N supply during a cotton season. Despite using an agronomic practice of splitting urea application to reduce losses and an optimal rate (232kg urea-N ha–1) for the experiment, the average fertiliser recovery was 32%, which indicates that soil N mineralisation is a key source of N for irrigated cotton production systems. A large amount of the fertiliser (62kgNha–1) was immobilised in the soil at the end of the season and during the season the soil supplied 159kgNha–1 to the plant via mineralisation. During the season, large N losses occurred from the field via the atmospheric, deep drainage and surface run-off pathways (143kgNha–1). The losses occurred directly after fertilisation, predominantly at the start of the season when the majority of the urea fertiliser was applied (180kg urea-N ha–1). This indicates that the form, placement and timing of the fertiliser did not synchronise with soil and crop N dynamics and irrigation practice. Over the course of the measurement season, based on the N inputs, losses and storage budget, a 42kgNha–1 soil deficit was observed. Further longer term work is required to quantify the magnitude and significance of the soil N stock across different systems.