Vessel traffic may have contributed to southern resident killer whales Orcinus orca becoming endangered. To determine the importance of this threat, we measured the behavior of southern residents in the presence and absence of vessels from 2003 to 2005 at 2 different sites along San Juan Island, Washington, USA. We observed activity states of killer whale schools using scan sampling and collected information on the number of vessels present at various distances from those. We use first-order, time-discrete Markov chains to estimate state-transition probability matrices under varying boat exposure conditions. Transition probabilities between activity states were significantly affected by vessel traffic. In addition, there was a reduction in time spent foraging, as estimated from the stationary state budget from the Markov chains, confirming an effect also previously observed in northern resident killer whales. If reduced foraging effort results in reduced prey capture, this would result in decreased energy acquisition. Each school was within 400 m of a vessel most of the time during daylight hours from May through September. The high proportion of time southern resident killer whales spend in proximity to vessels raises the possibility that the short-term behavioral changes reported here can lead to biologically significant consequences.