As part of the Essex Estuaries Initiative, the CEP was established with a management group of statutory bodies and as an advisory group to establish a Colne estuary strategy to work towards the social, economic and environmental well-being of the estuary area and its towns and villages. The key element of the strategy being partnership involving a wide range of local organisations and people.
In the early days of the partnership, Colchester Borough Council funded a post of 'Colne estuary officer' who coordinated the Partnership and liaised with numerous stakeholders. The Partnership has been successful in obtaining various sources of EU funding during its first 5 years, but recently funding restrictions have meant that CBC could no longer fund the Estuary Officer position. Since 2007 the CEP has been run through the offices of the Brightlingsea Harbour Commissioners .
Due to problems with inconsistent funding the Partnership undertook limited activities over recent years but since March 2009 the Department of Biological Sciences at the University of Essex has provided matching funds to create a role of a researcher to collate the extensive knowledge held within the University relating to the Colne and to co-ordinate with the Estuaries Officer at Brightlingsea to increase the activities of the CEP once more and to raise the profile of the group in relation to the management of the Colne and its habitats and by giving local stakeholders the opportunity to once more become involved in the management of their estuary and its resources.