In marine environments, urea is an important component of the biogeochemical cycle of nitrogen. The autochthonous and allochthonous sources (rivers, aquaculture, waste water input, etc.) of urea play a key role in urea cycles in adjacent coastal waters. Because urea is a specific marker to trace the sewage fluxes in coastal waters, we investigated urea associated with terrestrial source input and coastal water in Zhanjiang Bay (ZJB) during the time from November 2018 to July 2019, and the spatiotemporal urea distribution and the bioavailability of dissolved organic nitrogen (DON) based on urea concentration in the ZJB were explored. The results showed that the urea enrichment in coastal water was mainly due to discharge from urban sewage systems, rivers, and coastal aquaculture. The concentration of urea ranged from 1.14 to 5.53 μmol·L−1, and its mean value was 3.13 ± 1.02 μmol·L−1 in the ZJB. The urea concentration showed a significantly different seasonal variation in the ZJB (p < 0.05), and the highest and lowest concentrations were found in November 2018 and April 2019, respectively. Its high value appeared in the north and northeast of the ZJB, which were polluted by coastal aquaculture and agriculture fertilizer utilization. The range of urea concentration of terrestrial source inputs in the ZJB was 1.31–10.29 μmol·L−1, and the average urea concentration reached 3.22 ± 0.82 μmol·L−1. Moreover, the total urea flux surrounding the ZJB was 2905 tons·year−1. The seasonal terrestrial source of urea flux contributions had significant seasonal variation in wet, normal, and dry seasons (p < 0.05). The ZJB was subjected to a large flux of urea by estuaries and sewage outlet discharges. The seasonal urea concentration in all stations (>1 μmol·L−1) indicated that urea in the ZJB may have a bioavailable DON source. As a bioavailable nitrogen source, the ability of terrestrial source-derived urea to increase eutrophication should not be ignored in ZJB.