Mill Bay is situated on the western side of Saanich Inlet, a glacially-carved fjord that is approximately 24 km long and reaches a depth of 234 m.
Saanich Inlet is one of the best-studied marine basins in the world due to its unusual characteristics:
- There is little freshwater input directly into Saanich Inlet; most comes from the Cowichan River and the Fraser River at the mouth of the inlet (seaward side). Freshwater and salt water come into the inlet together (freshwater on top), which causes a phenomenon known as a reverse estuarine circulation.
- The inlet is naturally low in oxygen (hypoxic) for the majority of the year, primarily due to a 70 m sill at the mouth of the inlet, which restricts water inflow. When tidal mixing gets stronger during the winter, water is pushed over the sill, allowing the bottom waters to be replenished with oxygen.
The community-based observatory in Mill Bay, supported by Brentwood College School, is stationed at a depth of 8 metres. This observatory has several instruments including a CTD (measuring Conductivity, Temperature and Depth, as well as the salinity, pressure, and density of the water), an oxygen sensor, a fluorometer, and a camera. There is also a shore-based weather station in addition to the undersea instruments. Together, these instruments provide insight into the functioning of the bay, atmospheric-ocean interactions, benthic and water column biology, and near-shore water properties.