The £250m project to revamp the now derelict former International Garden Festival site includes the creation of a park, the restoration of the Chinese and Japanese gardens, improvements to lakes and waterways, a new pedestrian access point and improved parking and public transport facilities.
Other plans for the 40ha site include the creation of more than 1,300 homes as well as retail and office space.
Land Trust head of portfolios Alan Carter said Groundwork stood out in the application process as one of the most enthusiastic contenders to manage the gardens.
"It has already come up with some wonderful ideas for future uses of the site and its local network makes it perfectly positioned to involve the community," he said.
Pat Broster, executive director at Groundwork Merseyside, said the organisation was exploring progressive ideas. "We are looking forward to working with partners and engaging with the community in order to bring them to fruition," he said. Work on the Festival Gardens is expected to be completed in the spring.