The regulators investigation will seek to understand why the trusts finances have deteriorated and whether it has a credible plan to improve them.
It will also examine how the trust, which runs health care services in Warrington, Runcorn, Widnes and the surrounding areas, is working with other local NHS bodies to address its problems.
Paul Chandler, Regional Director at Monitor, said:
Patients in Cheshire rely on their local hospitals and we want to make sure that Warrington and Halton Hospitals can continue to provide quality care while effectively managing its finances.
We want to find out why the trusts finances have deteriorated and what can be done to fix them.
Monitor will announce the outcome of its investigation, and whether any regulatory action is needed, in due course.