The Port Authority of Pasaia collaborates in programmes for monitoring the quality of the water in the bay with different public authorities:
- With the Basque Water Agency (Agencia vasca del agua, URA) in the Monitoring network for the ecological status of the “Basque Country's transitional and coastal waters status monitorization” Network monitoring of the ecological status in transitional waters and coastal of the autonomous community of the Basque country"with three estuarine control stations. Sampling is carried out every year.
- With the Provincial Council of Gipuzkoa, in the “Analysis of the water quality and annual report on the state of the estuaries in Gipuzkoa” which includes sampling campaigns that cover different physical-chemical variables with six sampling stations for analysing the water quality in the "Oiartzun Estuary" every year.
The main waste sources present in Pasaia Bay come from the town of Donibane and the Txingurri irrigation channel, as well as the companies that operate within the port area and generate industrial waste or waste water that may contain contaminants, as in the case of the solid bulk storage area.
Responsibility for the waste from land to sea corresponds to URA, which controls the authorised waste and responds to any possible incidents of abnormal waste.
Following the work on the new fish market, in 2013 the waste from activities relating to fishing have been regularised through the corresponding waste authorisation.
The Port Authority of Pasaia is responsible for keeping the surface of the water in a good state of cleanliness. To do this it has a service featuring a cleaning vessel, which carries out the tasks of collecting floating solid and liquid waste within the port's waters. This waste is separated and delivered to an authorised manager.
Furthermore, the Pasaia Port Authority, through the Control Centre of the Port Police, centralises the processing of complaints received and assesses each case to decide whether certain measures need to be applied