The Porirua Harbour formed when westward flowing rivers were drowned by rising postglacial sea levels approximately 10000–14000 years ago. There is a tradition that the
1855 Wairarapa Earthquake caused tectonic uplift in the Pāuatahanui Arm of the inlet, changing the shoreline and reducing its navigability. However, according to George Eiby, the inlet always had limited accessibility, and the earthquake didn't significantly change the shoreline, with any changes likely coming from more recent sedimentation. Part of the Porirua Inlet was reclaimed for a causeway carrying the
North Island Main Trunk railway when the section between
Porirua and
Mana was straightened and double tracked. The new section of the
Kāpiti Line was opened on 7 November 1960. A new
Paremata Railway Station and bridge over the entrance to the Pāuatahanui Inlet were required. The line no longer followed the curves of the shoreline bays north of Porirua, and three shallow lagoons on the land side of the new causeway were created. When
State Highway 1 was re-aligned and straightened in the 1970s to run alongside the rail line, these lagoons were partially filled in.
Aotea Lagoon was developed into a recreational area, albeit very polluted. ==Recreation==