1999 was a year of changes and innovations. Bill Putnam stood down after twenty years as Chairman, and was followed in the role by Professor Clive Gamble. At the Head Office in Portway House, increasing staff numbers meant that office space was becoming more and more cramped. A decision was taken to build a single storey extension linking the old Operations and Medical Blocks. Work on this started in October 1999 and was finished by July 2000. 
The partnership between Wessex Archaeology and Oxford Archaeology was further cemented in 1999 by the creation of Oxford Wessex Archaeology (OWA). In this new arrangement they set out to investigate the archaeology of the M6 toll road near Birmingham and of the A120 in Essex. 
Meanwhile, Framework Archaeology continued work for BAA at Heathrow Airport, where evidence of activity from Mesolithic to medieval times was found and recorded. Work also started at Stansted Airport in Essex. A completely new recording system and database that would link all aspects of site recording (contexts, digital drawings, finds and environmental data etc.) were introduced for use on Framework sites. 
Closer to home, evaluations at the site for Southampton Football Club's proposed new stadium in St Mary's, showed that it lay partly within the area of the Saxon town of Hamwic, the forerunner of modern Southampton. Despite the site being criss-crossed and disturbed by the remains of modern gasworks buildings, the archaeology was important and merited excavation. This started at the end of 1999.