Bottom water intrusions are one of the major circulation features of Puget Sound, Washington. These intrusions supply oxygen and chlorophyll rich surface waters to the depth of Puget Sound providing a pathway for oceanic phytoplankton species into the Sound. In this paper we analyze observation on the formation of a deep-water intrusion at Admiralty Inlet, and characterize it for its hydrographical and bio-chemical properties. Subsequent observations, performed a week later within Puget Sound, provide information on bio-chemical transformation within the intrusive water. Most of the Chlorophyll and cyanobacteria-like cells are observed to decrease significantly in the intrusion. Phytoplankton respiration, however, explains only 30% of the reduction in oxygen within the intrusion, suggesting that respiration of additional organic material takes place within the deep water. Flow-cytometric analysis reveals three dominating groups of particles. One of these has optical characteristics similar to a coastal cyanobacteria and has a half-life in the dark of about 6 days. This characteristic makes it a good temporal tracer for the intruding waters. The predictability the sub-tidal circulation features in Puget Sound exhibited here as well as in other studies, suggests that it may be possible to maximize the flux of anthropogenic contaminant out of Puget Sound by timing their release and by modifying their density.