Warrington has become a hung authority after the ruling Labour group lost four seats to the Liberal Democrats.
The Lib Dems failed to oust Labour leader in St Helens Marie Rimmer
Labour remain the largest single party on the authority with 26 councillors, one more than the Liberal Democrats.
And they kept hold of Liverpool although they lost three seats to Labour candidates.
Two other councils - Chester and Sefton - have remained in no overall control, while the Labour party has retained control of both Halton and Knowsley.
Labour is also celebrating keeping hold of Ellesmere Port and Neston.
Labour is also the largest single party on Wirral Council but without a majority where the only change was the defeat of a UKIP candidate.
The party is still the largest single group on St Helens Council, but does not have an overall majority and the Lib Dems could still join with the Tories to run it.
However its leader Marie Rimmer kept her seat with a 457 majority despite a determined Lib Dem drive to oust her.
But in Halton Labour Mayor Peter Lloyd-Jones lost his seat to the Tories by 29 votes.
Mr Lloyd Jones is planning a formal appeal against the conduct of some of his opponents and alleged ballot irregularities.