Annual variations of inorganic nutrients such as nitrate(+nitrite), phosphate and silicate in association with thermocline were investigated in the upper 200 m of the water column at KODES Long-term Monitoring (KOMO) station in the northeast equatorial Pacific from 1995 to 2002. Global climatic disturbances such as El Nino and La Nina, should have affected KODES area during the study period. In 1995-97 and 2000-2002, a thermocline where temperatures rapidly decrease with depth, was formed at 50-70 m water depth. Nutrient depletion, specially for nitrate and phosphate, was extended down to approximately 50 m depth, which coincided with the surface mixed layer depth. In 1998 and 1999, however a very fluctuating thermocline was observed at 20-100 m water depth. In the photic zone (up to 100 m depth), depth integration of nitrate, phosphate and silicate ranged from 2.02 to $23.14;gN/m^2$, from 0.87 to $4.05;gP/m^2$ and from 35.67 to $176.21;gSi/m^2$, respectively. As a result of changes in the water column structures, nutrient concentrations also showed fluctuation parallel to the changes of thermocline in the study area.