In the end, the government's health bill passed with a whimper rather than a bang. There was no ministerial cave-in, no Lib Dem rebellion in the Commons. As the dust clears, a bill that was so passionately opposed slunk meekly into law. The government won, but no one is quite sure what kind of a victory it has achieved, or at what price.

It has been an exhausting, stop-start process for the staff who will continue to implement the reforms. They have faced uncertainty and delay over the past 14 months, and a lack of clarity about why the bill was needed. Now they have a year to prepare the NHS for the new world of GP-led clinical commissioning groups, more competition, a new NHS economic regulator (Monitor), local health and wellbeing boards and a new patient representative body (HealthWatch).

"It's a difficult situation," said Mike Farrar, chief executive of the NHS Confederation. "A lot of staff on the ground lack confidence in the bill, or say they don't like it, at a time when we need massive energy and commitment from staff. It makes it harder."

Health service staff are used to upheaval and improvisation, having experienced more or less permanent revolution over the past decade. But what made this different, said Farrar, was the complexity of introducing reform at a time when money is being taken out of the system. The NHS has to save £20bn by 2015. "In the short-term the major issues are going to be managing the NHS with less money and dealing with the consequences on priorities and quality of care."

Professor Chris Ham, chief executive of the Kings Fund, said funding pressures would come to the fore. "The reforms will not have a major impact in this parliament. But you will start to see trusts fail to meet four-hour accident and emergency waiting targets, you'll see a high level of bed occupancy, planned surgery being postponed."

The danger, said Ham, was that doctors and managers could become preoccupied with the changes rather than concentrating on efficiency and innovation the NHS so desperately needs. But even so, he has concerns that the new GP-led commissioning groups will struggle to be ready by April 2013. The bill may have passed but there is every chance some changes will stumble and be "distorted".

Already some critics are looking ahead to political battles over NHS cuts, which raise the possibility of GP rationing and hospital and ward closures. The introduction of Any Qualified Provider will almost certainly see more outsourcing of some services to the private sector. Some of the more established GP commissioning groups are expected to flex their muscles by switching care away from hospitals they do not rate, potentially threatening the viability of some.

Dr Kailash Chand, a GP and vocal opponent of the bill, said the reforms would be demoralising, not just for professionals but for patients, who would begin to see fewer treatments available to fewer people as the NHS cuts start to bite – with wealthier people able to "top up" treatments. "The rich really will be able to have much more. It's not just a postcode lottery, it's a taxcode lottery."

Both sides of the political divide were assessing the spoils after 14 months of battle. The coalition will be relieved that the bill that no one seemed to want has been forced through, even if the changes it introduces are complex and time-consuming, and clearly unpopular with staff and in some cases behind schedule.

The health secretary, Andrew Lansley, looks battered by his experience over the past year; abandoned, by and large, by the medical professionals he sought to put at the heart of the bill, and distrusted by some on his own side who fear he has singlehandedly retoxified the Tory NHS brand.

Lansley was infamously subjected to a cruel briefing by No 10, which said he should be "taken out and shot" for his failure to gain support for the bill. Some suspect Lansley's head will be served up in a summer reshuffle – the price for a fresh rapprochement between the prime minister, who effectively took control of the reforms last year, and the alienated clinical professions.

Labour has built up a head of steam over the legislation, aligning itself with a popular "drop the bill" motion. This has boosted its poll ratings. Labour also claims to have won key concessions in the Lords have strengthened the bill, from ensuring the secretary of state retains legal and political responsibility for the NHS, to strengthening the education and training of medical staff.

But it too realises it needs to take stock of the evolving pressures facing a shrinking NHS. As the party's former general secretary Peter Watt said this week: "Back to the future is hardly an inspirational rallying cry in a key policy area for Labour. Instead it needs to begin to set out what its vision for the NHS is."