The roles of intraseasonal Kelvin waves and tropical instability waves (TIWs) in the intraseasonal and low-frequency mixed-layer temperature budget were examined in an isopycnal ocean model forced by QuikSCAT winds from 2000 to 2004. Correlations between temperature tendency and other terms of the intraseasonal budget compare well with previous results using Tropical Atmosphere Ocean (TAO) observations: the net heat flux has the largest correlation in the western Pacific and zonal advection has the largest correlation in the central Pacific. In the central Pacific, the intraseasonal variations in zonal advection were due to both the zonal background velocity acting on the Kelvin wave temperature anomaly and the Kelvin wave's anomalous velocity acting on the background temperature. In the eastern Pacific, three of the four temperature budget terms have comparable correlations. In particular, the vertical processes acting on the shallow thermocline cause large SST anomalies in phase with the intraseasonal thermocline anomalies.

On intraseasonal time scales, the influence of individual composite upwelling and downwelling Kelvin waves cancel each other. However, because the intraseasonal SST anomalies increase to the east, a zonal gradient of SST is generated that is in phase with intraseasonal zonal velocity. Consequently, heat advection by Kelvin waves rectifies into lower frequencies in the eastern Pacific. Rectification resulting from TIWs was also seen. The prevalence of intraseasonal Kelvin waves and the zonal structure of intraseasonal SST from 2002 to early 2004 suggested that they might be important in setting the eastern Pacific SST on interannual time scales.