This study explored the variations in the characteristics of the trophic structure of Daya Bay island waters over the last four decades based on the survey findings and research data on biogenic elements (dissolved inorganic nitrogen (DIN), NO2−, NO3−, NH4+, PO43−, and SiO32−) in Daya Bay during 1985–2021. At this time, the DIN concentration increased from 21.14 µg·L−1 to 558.42 µg·L−1 (26.41-fold increase), whereas the SiO32− concentration increased by only 3.6-fold. The PO43− concentrations attained a peak in 2004 and experienced a steady decline over the rest of the survey period. The fractions of NH4+, NO3−, and NO2− in DIN changed from 0.45, 0.40, and 0.15 in 1986 to 0.26, 0.74, and 0.003 in 2021, respectively. Overall, the mean values of NH4+, NO3−, and NO2− accounted for 45.2%, 42.5%, and 12.3%, respectively. The N/P(DIN/PO43−) ratio in Daya Bay increased from 28.08 in the 1980s to 51.63 in the 2010s. Meanwhile, the nutrient limitation conditions showed a gradual shift from N-limited to P-limited conditions. According to the nutrient quality index (NQI) analysis, the trophic state level of Daya Bay waters fell into the oligotrophic category 30 years ago (1985–2002, NQI < 2), whereas it increased from the mesotrophic level in 2005 (NQI = 2.03) to the eutrophic level in 2019 (NQI = 3.33) over the last 20 years. The results based on the eutrophication index (EI) of Daya Bay waters were generally consistent with those based on the NQI, displaying that the trophic level of Daya Bay waters indicated an increasing trend from 2005 to 2019. Moreover, the assessment data in 2021 indicated a decrease in the NQI to 0.90, thereby attaining the oligotrophic level again. This may be related to the decrease in aquacultural area in the bay over the last two years. The correlation analysis among the DIN, PO43−, and nutrient levels of Daya Bay waters indicated that the input of nitrogen and phosphorus was the primary reason for the higher nutrient levels in the water bodies; among them, municipal sewage discharge, aquaculture, and atmospheric deposition from industry are the main factors for the over importation. This indicates that the changes in the biogenic element concentrations led to variations in the trophic structure and level of Daya Bay and may be attributed to population growth and the development of the seaside industry and agriculture in the region.