From the moment his name was floated as a candidate for the post of government chief scientific adviser, Sir Mark Walport became the front-runner. So few people were surprised when it was announced at the end of June that Walport, a 59-year-old immunologist who has spent the past decade as director of the Wellcome Trust, will be moving to Whitehall in April 2013 to take the top job in British science policy.

Under its past three occupants - Lord May, Sir David King and Sir John Beddington - the role has grown steadily in importance. While its primary function is to act as a personal adviser to the prime minister and the Cabinet, and to lead the Government Office for Science, it now sits at the pinnacle of a network of 22 departmental science advisers who operate across the whole of Whitehall. And the role has broader dimensions: to act as a champion for science within government and also as a communicator of evidence and uncertainties to the media and the wider public.

Walport enters the job with high expectations. Bold, decisive and at times forceful, he is a seasoned operator who knows his way around the corridors of Whitehall. During his successful tenure at the Wellcome Trust, he has been a vocal advocate for genomics research, open-access publishing and science education. He has also done a lot to promote public engagement and to foster links between the biosciences, the arts, the humanities and the social sciences, not least through the opening in 2007 of the Wellcome Collection, a popular free venue "for the incurably curious".

Walport's appointment has been widely welcomed. Sir Paul Nurse, president of the Royal Society, commented that "we have absolutely the right person for the job". But however talented, Walport may still find it a challenge to juggle the various demands of the role. On arrival he is likely to be met with a bulging in tray.

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Top of the pile will be funding. Another spending round looms, perhaps as soon as autumn 2013, and Walport will need to exert his influence inside the system to protect his share. Research council budgets, although suffering, have at least been maintained at flat-cash levels until 2015. But departmental research budgets have long been seen as a soft target by the Treasury. The imminent departure of Sir Adrian Smith, director general of knowledge and innovation in the Department for Business, Innovation and Skills, to become vice-chancellor of the University of London, adds to the climate of uncertainty. If Smith's role, which has traditionally been occupied by a senior academic, is handed to a civil service insider, the voice of the scientific adviser, as the most senior academic within Whitehall, becomes even more crucial.

A second priority will be shoring up the place of science and evidence within the processes of Whitehall reform. Francis Maude, as Cabinet Office minister, and Sir Jeremy Heywood as Cabinet Secretary, have both emphasised the need for more fundamental change in the way Whitehall operates, and the direction of travel was set out in last month's Civil Service Reform Plan. From a science policy perspective, the focus on "improving policymaking capability", the tentative commitment to a "NICE for social policy" (equivalent to what the National Institute for Health and Clinical Excellence does for healthcare) and the recent publication of a Cabinet Office paper on the use of randomised controlled trials in deciding on policy (co-authored by the science writer Ben Goldacre) are all encouraging signs. But structures for scientific advice have at times been too detached from wider Whitehall efforts to improve the policymaking process. Walport needs to ensure that these initiatives are better joined up, and position the network of departmental science advisers as models of good practice and agents of cultural change across Whitehall.

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A third challenge will be to act as a champion not only for the natural sciences but for the breadth of all that the academic community has to offer. Walport's track record at Wellcome is positive in this regard, but as the British Academy has pointed out, there remains an implicit (and often explicit) hierarchy of disciplines within the policy process. Many of the issues that chief scientific advisers have to grapple with, from climate change to food security and ageing to obesity, require insights from across the disciplinary landscape. A good adviser recognises the importance of politics in science, in shaping what counts as evidence and authority, as much as the importance of science in politics. It will be vital for Walport to demonstrate early on his openness to the contribution that different perspectives make to an effective advisory system - including those of the arts, humanities and social sciences, and also civil society and the wider public.

Finally, there is the ever-present threat of the unexpected - what we might sum up as mad cows, ash clouds and asteroid strikes. At some point in Walport's time as government chief scientific adviser, a crisis will erupt that places scientific credibility on the line. This will be the real test of his judgement and leadership. Solly Zuckerman, the zoologist who first occupied the post under Harold Wilson, loved the job but was forced to admit that "the human mind cannot operate lucidly and with genius in the atmosphere of a committee". If he can manoeuvre effectively within Whitehall, if he knows when to lead and when to listen, and if he can still find the space to display the odd flash of genius, Walport has the potential to be a great scientific adviser.