The sensitivity of the thermal structure of the equatorial Pacific and Indian Ocean pycnoclines to a model's representation of the Indonesian Straits connecting the two basins is investigated. Two integrations are performed using the global HOPE ocean model. The initial conditions and surface forcing for both cases are identical; the only difference between the runs is that one has an opening for the Indonesian Straits which spans the equator on the Pacific side, and the other has an opening which lies fully north of the equator. The resulting sensitivity throughout much of the upper ocean is greater than 0.5°C for both the equatorial Indian and Pacific. A realistic simulation of net Indonesian Throughflow (ITF) transport (measured in Sverdrups) is not sufficient for an adequate simulation of equatorial watermasses. The ITF must also contain a realistic admixture of northern and southern Pacific source water.