Stephen Winter , head of the 3a-rated computer science department at Westminster University, was hoping to see money made available for improving departments.
He said: "Our department has steadily improved, which follows sector performance, but we have not been rewarded for our improvement, which suggests there is something wrong with the funding model.
"If the £1.25 billion helps to resolve this and we see our hard work rewarded too, then the government's investment will be a good one as computing is key to the continued economic health of this country."
Trevor Davies , dean of the University of East Anglia's 5* environmental sciences department, said: "After two decades of despair across the UK's university science community, it is encouraging to think there is now more petrol in the tank.
"We can begin to rebuild the engine, for which we must give credit to the government, but we are still far from having a full tank. This modest start will help begin the serious maintenance to our 1960s buildings and the replenishment of equipment."
Professor Davies said that the increased minimum stipend for PhD students would encourage the brightest to consider a career in science.
Chris Neville-Smith , a PhD student at Durham University's 5* chemistry department, said: "The increase (in stipends) is definitely welcome and will allow us to compete with graduate starting salaries in other sectors.
"Most of my peers got a job that had nothing to do with their degree. PhDs should be funded for four years not three as the average PhD student takes three-and-a-half years to complete and will often get into difficulty in the final year. Students should put some of this extra money away for the fourth year.
"The government's real task, though, is to increase the supply of quality BSc graduates. We need people academically, not financially, capable of doing a degree to ensure a flow of PhD students."
Chris Hawes of Oxford Brookes' biological and molecular sciences department is acutely aware of the need to get young people interested in science to maintain the supply of scientists.
He said: "You have to get schoolchildren interested, otherwise you can forget the research. The increase in science funding for schools will feed universities, which is a good thing."
As the head of a 3a department, Professor Hawes hopes "the research assessment exercise is funded properly in the future to see money reaching down to the 3a and 3b departments".
Jeff Kramer , head of Imperial College's 5*-rated computer science department, said: "It would be perverse not to welcome the announcement, but the devil is in the detail and currently we have little detail. My fear is there will be strings attached to the cash which create more red tape.
"Hopefully the chancellor will keep his word and high-performing departments will get rewarded, giving us more autonomy and the ability to set our own agendas."
He welcomed the increase in salaries for postdocs. "Money for PhD students is our life-blood. In a recent recruitment round we attracted world-class applicants but failed to get the candidate we wanted - we couldn't compete with salaries in the US."
Bob Rees , a cancer vaccine researcher at Nottingham Trent University's 5-rated department of life sciences, also welcomed the money for researcher pay. He said: "Our department loses a third to half of our PhD students to the US because we can't offer them a real career track, or we don't have the funds to renew contracts.
"This money could make a significant difference if it was used to help create proper research/ teaching posts for younger scientists.
"The funding needs to support up-and-coming scientists, infrastructure and equipment and help retain scientists."