Abstract An examination of model water masses in the North Pacific Ocean is performed in the Community Climate System version 3 (CCSM3) and its ocean-only counterpart. While the surface properties of the ocean are well represented in both simulations, biases in thermocline and intermediate-water masses exist that point to errors in both ocean model physics and the atmospheric component of the coupled model. The lack of North Pacific Intermediate Water (NPIW) in both simulations as well as the overexpression of a too-fresh Antarctic Intermediate Water (AAIW) is indicative of ocean model deficiencies. These properties reflect the difficulty of low-resolution ocean models to represent processes that control deep-water formation both in the Southern Ocean and in the Okhotsk Sea. In addition, as is typical of low-resolution ocean models, errors in the position of the Kuroshio, the North Pacific subtropical gyre western boundary current (WBC), impact the formation of the water masses that form the bulk of the thermocline as well as the properties of the NPIW. Biases that arise only in the coupled simulation include too-salty surface water in the subtropical North Pacific and too deep a thermocline, the source of which is the too-strong westerlies at midlatitudes. Biases in the location of the intertropical convergence zone (ITCZ) and the southern Pacific convergence zone (SPCZ) lead to the opposite hemispheric asymmetry in water mass structure when compared to observations. The atmospheric component of the coupled model acts to compound most ocean model biases.