The organization announced last week that its Queen's Quay revitalization project is more than $35 million over budget.
Waterfront Toronto Chair Mark Wilson said his organization has made it clear to both the government and the public that costs had grown due to issues like discovering unidentified pipes, unconnected storm sewer pipes and sinkholes.
"This is not a runaway project," Wilson said.
"This is a project that is carefully, professionally and well managed."
Deputy Mayor Denzil Minnan-Wong, one of the organization's biggest critics, now has a seat on the organization's board from which to voice his concerns.
Minnan-Wong has called for the board to curb spending on expensive materials like granite and also wants the board to be more transparent.