The firm has taken the £35m job to build a major manufacturing facility at the site, in a scheme called Project Perch, next to a proposed International Trade Centre for Chinese firms.
It will build the warehouse building on land to the north of Beaufort Road and to the east of Wallasey Bridge Road at West Float, Birkenhead.
Once finished the building will be used for the manufacturing of large components within the energy sector.
The wider Wirral Waters project proposed by Peel Group was granted outline planning permission in 2012.
Morgan Sindall is also presently on site building the new Wirral Metropolitan College Campus under an £8m contract, which was hailed as the first building project on the major redevelopment plan.
Walker Sime is managing the project on behalf of Peel. Further upstream on the River Mersey, Peel owns a majority stake in ship repairer and engineering business Cammell Laird, which makes parts for the offshore wind and nuclear industries.