The seasonal-spatial variations of nutrient and Chlorophyll-a around the Pearl River Estuary (PRE) and adjacent coastal waters were investigated based on the survey data collected at 25 stations in July, October 2006 and March 2007. The relationship were examined between the ratio of nitrogen to phosphorus (DIN:PO₄-P and TN:TP), the Chlorophyll-a concentration and the diversity of phytoplankton species, and the effects of nutrient limitation on the phytoplankton growth were taken into account. The results indicated that: 1) the concentrations of nutrients and Chlorophyll-a had a strong seasonal and spatial variation. Seasonally, the mean concentrations of TN and TP in March (spring) and July (summer) were higher than those in October (autumn), and an obvious special variation of nutrient concentrations had been found in summer and spring, while it were more even in autumn. Spatially, much lower nutrient concentrations in Daya Bay and Guanghai Bay were found in comparison with the high nutrient concentrations in Pearl River Estuary. 2) The nutrient concentrations in the study area were rather high, and exceed the China national seawater water quality standards remarkably, especially in summer. The mean DIN concentration was about 0.99 mg/L, which was more than twice of the water quality standard Category 4, the mean PO₄-P concentration was about 0.021 mg/L, and the mean ratio of DIN:PO₄-P was about 130 far above the Redfield ratio (16:1), which is the optimum value of phytoplankton nutrient requirements. With a significant enrichment of nitrogen relative to P, there was excess of N and potentially P limitation in coastal waters of PRE and nearby seas. Chlorophyll-a concentration showed a better correlation with nutrients, pH, and temperature in this region. 3) During the investigation in spring and summer, phytoplankton density distribution was variable, with major dominant species (Skeletonema costatum). The phytoplankton biomass were high at the stations where the N:P ratio was high while the diversity index was usually low. Thus, the growth of phytoplankton wasn't inhibited in the high N:P ratio area. In that area, the phytoplankton biomass distinctly increased due to the emergence and growth of dominant species. It was shown that the demand for nitrogen and phosphorus nutrient might vary greatly with the different types of phytoplankton; as a result, the variation of the ratio of nitrogen to phosphorus might cause the differential responses between growth rates of various phytoplankton species, resulting in a change in phytoplankton community structure. The effect of N:P ratio on phytoplankton should be taken into account in the further water management.