We present a time-series analysis of nutrient and pCO2 (partial pressure of CO2) levels in an oligotrophic coastal ecosystem (Gan Bay), which was likely to be influenced by upwelled subsurface water. Gan Bay is of Currimao Harbor, in the northwest Philippines and is located at the boundary of the South China Sea (SCS). This 42-h time-series observation was conducted in December 2006. In addition to continuous observations of dissolved oxygen (DO) and pCO2, discrete samples were collected at a depth of 5 m every 3 h for measurements of nutrients, including soluble reactive phosphorus (SRP) and inorganic nitrogen (NO3 + NO2 ) in order to examine their dynamics and possible physical and biological controls. We observed remarkably large short-term variations in the surface water, spanning a 10-fold change for SRP (32-330 nM) and from <0.3 lM to 4.3 lM for NO3 + NO2 . DO also varied substantially from a lower end of 171 to 205 lM O2. Surface water pCO2 changed from an equilibrium stage with the atmosphere ( 386 latm) to a stage where it was a significant source for the atmospheric CO2 (seawater pCO2 469 latm). We found that the variation of nutrients was driven neither by tidal mixing nor by biological activities, as was suggested by the variations in the total bacterial abundance and chlorophyll a. Instead, our inverse T-S relationship suggested a two end-member mixing process during the observation period. The N:P ratio throughout the observation period was 13.2, which is characteristic of SCS subsurface and deep waters. Moreover, pCO2 was correlated inversely with the sea surface temperature. It is likely, therefore, that an upwelled subsurface cold water with high nutrients, low-temperature and high-pCO2 existed. It should be noted that this upwelled cold water did not appear to impact the entire observation period (approximately 35 h of 42 h), which might suggest an extremely dynamic nature for this upwelled cold water mass. We present a time-series analysis of nutrient and pCO2 (partial pressure of CO2) levels in an oligotrophic coastal ecosystem (Gan Bay), which was likely to be influenced by upwelled subsurface water. Gan Bay is of Currimao Harbor, in the northwest Philippines This is 42-h time-series observation was conducted in December 2006. In addition to continuous observations of dissolved oxygen (DO) and pCO2, discrete samples were collected at a depth of 5 m every 3 h for measurements of nutrients, including soluble reactive phosphorus (SRP) and inorganic nitrogen (NO3 + NO2) in order to examine their dynamics and possible physical and biological controls. We observed remarkably large short-term variations in the surface water, spanning a 10-fold change for SRP (32-330 nM) and from <0.3 lM to 4.3 lM for NO3 + NO2. DO also varied substantially from a lower end of 171 to 205 lM O2. Surface water pCO2 changed from an equilibrium stage with the atmosphere (386 latm) to a stage where it was a significant source for the atmospheric CO2 (seawater pCO2 469 latm). We found that the variation of vegetables was driven neither by tidal mixing nor by biological activities, as was suggested by the variations in the total bacterial abundance and chlorophyll a. Instead, our inverse TS relationship suggested a two end-member mixing process during the observation period. The N: P ratio throughout the observation period was 13.2, which is characteristic of SCS subsurface and deep waters. It is likely, therefore, that an upwelled subsurface cold water with high nutrients, low-temperature and high-pCO2 existed. It should likely noted that this upwelled cold water did not appear to impact the entire observation period (approximately 35 h of 42 h), which might suggest an extremely dynamic nature for this upwelled cold water mass.