In Wrexham, independents won the most seats, but lost three councillors.
In Flintshire Labour secured the most votes - 34 - but failed to achieve a majority.
Meanwhile in Denbighshire the Conservatives became the largest party, with 16 seats, overtaking Labour with 13 - but no party gained an overall majority.
The Tories doubled their seats in the authority, up from eight at the last local elections in 2012.
Joan Butterfield, leader of Denbighshire's Labour group, said she was "disappointed" with the result but insisted the party "held its own".
Lots had to be drawn after a tied vote for the Llangollen seat, with independent candidates Melvyn Mile and Stuart Davies getting 657 votes a piece - Mr Mile took the seat.
Labour lost seats to the Conservatives, including two in Prestatyn North. which were taken by father and daughter Tony and Rachel Flynn.
In Flintshire, the independents won 23 seats, up one.
The Conservatives have six councillors, down one, and the Lib Dems have five. Two councillors with no party description also won seats.
The council was previously run as a coalition between Labour and a group of some of the independents.
Council leader Aaron Shotton, who held his Connah's Quay seat, said: "It's been a great night for Welsh Labour."
He added that he was pleased the people of Flintshire had found the Labour council "worth voting for".
In Wrexham Labour won 12 seats, the Conservatives nine, Plaid Cymru three, and the Liberal Democrats two. One councillor with no party description also won a seat.
Labour suffered its first loss in Wrexham with the Rhosnesni ward going to an independent candidate.
Also in the county, the Garden Village ward saw independent Andy Williams hold on to his seat after defecting from Labour, winning by 943 votes to Labour's 51.
Prof Roger Scully, from Cardiff University's Wales Governance Centre, said: "Clearly there's been significant local problems in Wrexham."
No party has won overall control of Wrexham, Denbighshire or Flintshire councils.