The long term variation of nutrient structure in the southwest part of Daya Bay from 1982 to 2002 is analyzed in this study. The dissolved inorganic nitrogen (DIN) has increased steadily, phosphate has a trend of decrease from the 1980s to the end of 1990s and slightly increased after 2000, while silicate fluctuated at high level ~20μmol·L^-1 in different years. The nutrient atomic ratios also changed in this period: N/P ratio had a trend of increase, Si/N ratio decreased, and Si/P ratio increased slightly. These long term variations of the nutrient concentrations and their atomic ratios suggested that the nutrient limiting factor for phytoplankton growth could turn to phosphate limitation from nitrogen limitation in the last decade. The growth of phytoplankton is likely limited by nitrogen in spring and winter while by phosphate in summer and autumn. The spatial distribution in the southwest Daya bay shows the higher DIN concentration inside the Dapeng'Ao cove than that outside the cove, and phosphate concentration inside the cove is lower than that outside since 1997.