Yakamia Creek enters Oyster Harbour on its western shore just south of Bayonet Head. The creek is relatively small and drains farmland and urban areas of Albany. At the mouth of the creek silt has built up and a shallow, vegetated delta has formed. This is likely to be acting as an efficient, natural, nutrient filter, trapping nutrients before they get to the harbour. The reduced water flow around the delta, because of the vegetation, has caused periodic flooding of nearby farmland. There has also been increased run off because the creek's catchment has been urbanised.

Limeburners Creek enters Princess Royal Harbour on its southern shore. The creek drains an area where rain filters through the ground and goes into underground water supplies (this is known as a `groundwater recharge area') within the South Coast Water Reserve, which is administered by the Water and Rivers Commission.

A number of agricultural drains enter Princess Royal Harbour on its western shores. These include Taylors Drain, Robinson Estate Drain and Moreys Drain. About 18 urban drains maintained by the Town and the Shire of Albany also drain into Princess Royal Harbour.