Long‐wave theory is used herein to analyze circulation in weakly stratified and partially mixed estuaries. Unlike the highly stratified systems considered in part 1, the flows considered here have only a minimal tidal‐frequency internal wave component. These estuaries may therefore be modeled as the sum of weakly interacting barotropic and baroclinic modes. The dominant factors driving the residual flow are finite amplitude barotropic effects in weakly stratified estuaries and a combination of barotropic effects and steady horizontal density gradient forcing in partially mixed estuaries. The dominant vertical exchange mechanism in the weakly stratified case is bottom boundary‐induced turbulence, and that in partially mixed estuaries is believed to be random internal wave interactions. A model of the Columbia River Estuary under weakly stratified conditions accurately predicts the observed residual velocity and salinity fields, and the tidal amplitude at which a transition to a highly stratified state takes place. The partially mixed state is unstable in the Columbia River Estuary because the tides and buoyancy input are both too s