Clark, who has been the paper's financial correspondent for more than two years, plans to give more of a consumer focus to the transport coverage.
He replaces Keith Harper, who died in May after a short battle against cancer. He had been at the paper for 40 years.
Clark said: 'The agenda is moving. Rail will have a lower profile in the near future. Road transport issues, such as congestion charging and emissions, are set to come to the fore.
'The agenda has been dominated by railways. There will be more on cars and aviation in the next few years. The democratisation of air travel through budget airlines has made it more accessible to the man in the street, ' he added.
Harper was well known for breaking transport stories with a political and financial angle. Clark said: 'The coverage here has been very political. My background is as a City journalist but I am relatively new to politics.'
He has already written for The Guardian G2 supplement on airport proposals and said: 'There is scope to do more on the features side.'
The transport brief is split between the City and home desks, although Clark will report to financial editor Paul Murphy. 'There is plenty of overlap,' Clark said.
Political editor Michael White continues to cover Westminster-based transport developments, while Kevin McGuire will carry on writing about labour issues, such as Tube strikes.
Approaches from PROs are welcome, said Clark. 'But I've noticed you get a lot of local stuff that is not really of interest. It has to be of national interest,' he added.
Before joining The Guardian, Clark was editor of The Daily Telegraph's share tipping column, Questor. He has also worked at Sunday Business and World Link, the magazine of the World Economic Forum.