While Cardiff University remained the best-placed Welsh university in the annual Complete University Guide, it fell from 23rd place last year to 31st.
Swansea University fell three places to 45th.
However, Bangor climbed six spots to 58th and Cardiff Metropolitan moved up 19 spots to 79th.
With Cardiff Metropolitan being Wales' most improved institution on the list, its deputy vice-chancellor, Jacqui Hare, said the university was "really proud".
"The increase in our position in this independent ranking reflects our significant investment in the student experience here at Cardiff Met," she added.
The guide, which has been running since 2008, uses 10 measures to rank the top 125 universities across the UK.
It rates them all on entry standards, student satisfaction, research quality and graduate prospects, among other criteria.
Aberystwyth University maintained its 87th place ranking from last year, while University of South Wales fell from 100th to 102nd and Wrexham-based Glyndwr University dropped 13 places to 123rd.
The merged University of Wales, Trinity Saint David, which had been unranked since 2013, fought its way into the list at 125th.
The top three was unchanged from last year, with Cambridge University first, Oxford second and the London School of Economics third.
This year's Complete University Guide suggested Welsh universities have the highest student-staff ratios of any UK nation at just over 19 students per member of staff, compared to the UK average of 17.
It is one of several guides ranking the best institutions, with the latest Times Higher Education world university rankings due out on Wednesday.
Other barometers include the Research Excellence Framework, which rated almost a third of research by Welsh universities as being of "world-leading" quality when it was last released in December 2014.
Wales' top two universities lost ground in the latest higher education league table - with their Welsh rivals enjoying mixed results.