Waters will take over in November from the charity’s co-founder Bryn Parry, who announced in April that he would stand down by the end of 2016 after nine years in the role.
Waters has been in charge at The Poppy Factory, which provides employment for disabled veterans, for the past six years.
She was previously business director for the student accommodation business The Unite Group and has also worked for the Automobile Association in a variety of roles.
A spokesman for the charity was unable to confirm how much Waters would be paid. A statement issued on behalf of the trustees said H4H was among the lowest-paying of the major charities and this would not change when Waters was in post.
According to its most recent set of accounts on the Charity Commission website, the charity’s highest earner, who is not named, was paid between £100,001 and £110,000 in the year to the end of September 2015.
Help for Heroes had an income of £41m in 2014/15 and employed an average of almost 400 people over the same period, its accounts show.
Alex Scott-Barrett, chair of Help for Heroes, said: "Melanie brings with her energy and a proven track-record of results.
"Experienced in both the commercial and charitable sectors, she is a natural leader with expertise in both strategic and operational areas; this will be crucial as the Help for Heroes team drive the next stage of the charity’s development."
Waters said in a statement that Help for Heroes had brought a new energy to the armed forces charity sector.
"The organisation is known by both its beneficiaries and supporters for its uniquely positive culture and the open, easy-to-access support that it offers," she said.
"I am delighted to have been appointed by the trustees to lead the organisation and I plan to build upon the incredible work of the co-founders and the wider dedicated Help for Heroes team as the charity enters its tenth year."
Parry and his wife Emma, who co-founded the charity, will act as ambassadors for the charity from November.