Due to the intensive human activities and rapid economic development during the past few decades, the anthropogenic sourced nitrogen (N) input into coastal waters has increased dramatically. In this study, the net anthropogenic nitrogen input (NANI), including the deposition of atmospheric N, the application of N fertiliser, the fixation of biological N, and the net N inputs from food and feed, into the Zhanjiang Bay watershed from 1978 to 2018 were estimated using statistical data, and the driving forces were analysed using the Logarithmic Mean Divisia Index (LMDI) factor decomposition approach. The results show that the NANI dramatically increased from 5269 to 20 639 kg N km−2. The cause of this increase was related to high input from N fertilisers and the net food and feed N input (with average contributions of 56.45% and 41.42%, respectively), which was accompanied by rapid economic development in Zhanjiang Bay. The output from the LMDI illustrates that the cause of the changes in the NANI was a shift in the dietary structure instead of an increase in the human population, which suggests that the impact of human population on the increase in the NANI using simple relational analysis may be overestimated. Remarkably, we found that the N from aquatic protein and animal protein comprised a significant proportion of the total N consumption in this coastal city, which differs from previous studies of inland cities. This is likely due to the fact that aquaculture is significantly developed in this coastal city.