Abstract: Minjiang Estuary is an important economic development area in Fujian Province, and the past survey data on the water quality and environment of the estuary can no longer reflect its recent trend and pollution sources. To provide scientific support for comprehensive pollution management, this study analyzed monitoring data (2015–2022) from national and provincial seawater monitoring stations in the coastal waters of the estuary. Utilizing the seawater quality assessment system and principal component analysis (PCA), we investigated the spatiotemporal distribution characteristics of water quality and identified pollution sources. Results show that temporally annual water quality variations were inconsistent, with an overall improvement after 2019. Seasonal changes showed that the water quality is better in summer, than in autumn and spring. Spatially, water quality exhibited a pattern of poorer conditions near the estuary shoreline and better conditions offshore, with the highest water quality observed in the northeastern and eastern offshore areas. Five principal components were extracted from 12 monitoring factors, achieving a cumulative variance explanation rate of 79.87%, where inorganic nitrogen emerged as the dominant factor. Flux analysis of pollution sources revealed a negative correlation between pollutant loads from inflow rivers and the proportion of high-quality seawater, highlighting the significant impact of terrestrial pollution. Urban and rural domestic wastewater sources were identified as the largest contributors. This study provides critical insights for targeted pollution control strategies in Minjang Estuary.