Puget Sound is a fjord-like estuary in which bottom-water intrusions are a dominant circulation feature that play a major role in the replacement of water below sill depth within the estuary. New observations on the inside and outside of the entrance sill show that while intrusions occur during neap tides as previously thought, the onset of the intrusions occurs before the minimum in the neap tides. Calculations using a model with a balance between the longitudinal pressure gradient and vertical mixing suggest the onset is influenced by fluctuations in the horizontal density gradient caused by salinity variations across the sill. They also show that the resultant bottom inflow can be further modified by strong surface winds. Deep salinity changes seaward of the sill in the Strait of Juan de Fuca estuary appear to be the result of storms on the Pacific coast causing reversals of surface flow and variations in deep flow more than 135 km from the coast. Although Puget Sound is a glacially carved estuary, flow over the entrance sill in Admiralty Inlet has characteristics which resemble coastal plain estuaries; thus, these studies may have more general applications to time variations in lower layer flow at the mouth of other estuaries.