During the 1950s and ’60s, coastal engineers and coastal oceanographers focused on different problems with regard to estuaries. Coastal engineering problems related mostly to stability of tidal inlets, land reclamation and the closure of estuaries and bays for storm surge protection. Solving these problems required knowledge of tides and tidal currents. In contrast, coastal oceanographers tended to concentrate on tidal mean properties including salinity, stratification, gravitational circulation. While coastal engineers derived their tools from hydraulics, coastal oceanographers relied on geophysical fluid dynamics.

In the seventies the coastal engineers started to face different types of problems relating mostly to water quality. Because water quality is largely determined by tidal mean motions, the coastal engineers began to seek help from coastal oceanographers. As a result of this the coastal oceanographers detected an interest in their work that had been absent in the community of blue water oceanographers.

The logical place for the two disciplines to meet and exchange ideas seemed to be the biennial International Conference on Coastal Engineering (ICCE). Unfortunately, the forum of the ICCE became increasingly focused on the nearshore, relegating estuarine problems to the status of stepchild. It was at the ICCE of 1976 that a small group of coastal engineers and coastal oceanographers realised that their interests would be better served by a specialty conference focusing on the physics of estuaries. The idea was to have this conference at the same venue and either directly preceding or following the ICCE. This idea ultimately was abandoned because it was difficult to find host institutions in some of the places where the ICCE was held.
With the intent of focusing on estuaries, the first conference was organised in September 1978 in Hamburg. The second conference did not take place until 1984 in Miami. Since 1984 conferences have been held every two years. With the inclusion of physics of coastal seas in 1990, the conference series became known as PECS. A complete list of the conferences, chairpersons and host institutions is given below.

PECS has a Steering Committee consisting of the chairpersons of the previous meetings. The Committee ensures that future conferences adhere to the above mentioned objectives. The board also selects the venue of future conferences. Organising a conference and publishing conference papers is the sole responsibility of the local organising committee.