In September 2005 the European Parliament and the Council adopted Directive 2005/35/EC (since amended by Directive 2009/123/EC) on ship-source pollution and on the introduction of penalties, including criminal penalties, for pollution offences. The Directive tasked EMSA to "work with the Member States in developing technical solutions and providing technical assistance in actions such as tracing discharges by satellite monitoring and surveillance."

In early 2006, EMSA consulted industry and the national authorities of the EU Member States and coastal EFTA States in order to collect information on existing operational surveillance resources and further requirements for oil pollution monitoring. Based on feedback received during the consultation as well as from other relevant organisations, such as the European Space Agency, EMSA launched a procurement process in April 2006.

As a result of the procurement process, EMSA agreed a number of contracts for three year periods (later extended by one year). There are two different types of contract which underpin the CleanSeaNet service: 1) for the acquisition of satellite image licences; and 2) for the provision of oil spill monitoring services.

The following contracts for were agreed for satellite image licenses:

• Contracts for licenses for the European Space Agency's ENVISAT satellite were signed on 18 December 2006 between EMSA and Eurimage S.p.A. .
• Contracts for licenses for the Canadian Space Agency's RADARSAT-1 and RADARSAT-2 satellites were signed on 2 February 2007 between EMSA and MDA Geospatial Services Inc.

The following contract was agreed the provision of oil spill monitoring services:

• A contract for the provision of oil spill monitoring services was signed on 18 December 2006 between EMSA and a consortium of 3 companies: Kongsberg Satellite Services AS, Telespazio S.p.A and Edisoft.

Following the tender process and agreement of contracts with satellite image and service providers, the CleanSeaNet service became operational in April 2007, providing analysed satellite images to 15 EU coastal states.

Due to intensive use of CleanSeaNet by Member States, additional commitments and payments were made in 2008 and 2009 to meet the operational demand. The service has been extended several times. Some of the key developments include: the delivery of RADARSAT 2 images launched in December 2007; the entry into service of the Azores ground station; the provision of vessel traffic information (from regional AIS servers and via SafeSeaNet), the provision of vessel detection information and the link to backward and forward propagation oil spill models. As a result, CleanSeaNet is the most comprehensive oil spill monitoring service in Europe today, and supplies over 2,000 images a year to the 26 participating States.