Corporate affairs head Helen McCullum this week confirmed the new structure will be in place within weeks, and will see the creation of four separate teams.
These will be external and community relations, corporate relations, government relations and a communications advisory service.
The new structure, which boosts the directorate by five to a 65-strong team, replaces the previous six teams of media, corporate comms, public affairs, parliamentary affairs, EU and international affairs, and education.
'We've made it more streamlined so that the teams have a broader remit and can be more effective,' she said.
The communications advisory service is seen as one of the most innovative developments. For the first time a designated team has been created to advise many of the agency's 11,000 staff on PR.
This is expected to be most useful to technical staff dealing with industry-specific journalists and workers at a local level.
Three of the team heads have now been recruited. Liz Thompson has joined from the Countryside Agency, where she was head of knowledge management, to head external and community relations; Adrian Long, formerly of the Soil Association, heads corporate relations, and the communications advisory service is led by Robin Chatterjee. The government relations head post is still vacant.
McCullum said that a priority was to drive through an attempt to increase understanding of the agency's work: 'We have found that there is a high awareness of the agency but a low understanding of what it does.'
The restructure had put on hold an attempt last year to hire agency support for PR work, but McCullum has revealed that this is now set to resume in May when a search will begin for agencies to join a 'small roster'.
'Different parts of the Environment Agency were using agencies - we wanted to create a clearer system,' said McCullum.
Another pitch is also likely for a brand development specialist, 'to assist on elements of the brand'. She stressed that the aim was not a complete overhaul of the brand.
The Environment Agency has a brief to protect, improve and manage the environment. One of its most high-profile areas has been flood defence.