The Trust, launched this week, has the aim of raising participation levels, increasing spectatorship and doubling the media coverage of women's sport through distribution of grants to individuals and groups.
Watkins, who won the double sculls with Katherine Grainger at last summer's Olympics, is patron of the Trust and is a firm believer the excitement and interest in women's sport seen last summer demonstrates that, with the right approach, real progress can be made in this area.
"After the Olympics we had this sense of excitement and momentum in women's sport. I wanted to capitalise on that and keep it going so when I was asked to become involved I thought 'this is what I've been waiting for'," Watkins told Sky Sports.
"It would be a terrible shame if we lost this momentum, so I'm thrilled this organisation is starting up to keep it going."
The Trust has been backed by a diverse range of elite female athletes and Watkins hopes their support will give the organisation the traction and attention it needs to make a difference.
"I really want to do something for the up and coming athletes and I realise the power a good role model can do," she said.
"The Trust will give grants to up and coming athletes and people participating at sport at various levels - that's not something that's been done before specifically for women.
"It also works with businesses and connects people who have a common belief women's sport can be a force for good in this country.
"The Olympics showed us that it isn't that people aren't interested in women's sport or don't want to sponsor women's sport, it just isn't always out there and people don't know who is who.
"We need to get that message out there and the rest will follow."
Kelly Simmons, the Football Association's' Head of National Game and Women's Football, has seen first-hand how increased media exposure can lift a sport. Since Team GB's run to the quarter-finals of the women's Olympic football tournament there has been a significant upturn in the game's fortunes in this country.
"We've seen a real transformation since 2012, with the success of the GB women's football team," said Simmons.
"The Olympics took it to a brand new audience and since then we've seen broadcast deals for the game and new commercial partners coming in.
"But there's still a lot to do around women's sport generally. It's important we all work together to build on 2012 and keep the movement going."
The WST will be attracting new funding into women's sport, providing multiple routes for corporate partners and individuals to donate. A Grants Panel, chaired by Team GB hockey captain Kate Walsh, will shortlist applicants before those who have donated have the chance to vote on where their money is spent.
Further explaining the rationale for establishing the Trust, one of its founders, Tammy Parlour, (herself the founder of a martial arts academy) said: "Like many others, I was hugely inspired and moved by the incredible impact of so many strong female sports role models during last year's Olympic Games. We want the WST to build on this, and support the legacy for women's sport in the UK. Sport is one of the most important public arenas and has the potential to shift how women are seen and how they see themselves."
Kelly Smith MBE joins Anna Watkins as a Patron, with other athlete supporters including Shelly Rudman, Jonathan Edwards and Liz Yelling, along with a number of high profile female business leaders including Justine Roberts, the Founder and CEO of Mumsnet.
To find out more about the Women's Sport Trust and how you can get involved visit www.womenssporttrust.com