The Division Four South East side had started slowly but grew into the game, their second half performance seeing them pull clear to seal the win.
Fishguard had actually led at the break, James Griffiths scoring all of the Seagulls' points with a converted try and a penalty. But Richie Lewis got the Ducks back into it and second half tries from David Gibbs, Brendan Lyons and Nathan Bruford sealed the Bowl trophy.
Edward Bendall scored a late consolation for Fishguard but it was not enough.
After a scrappy opening 10 minutes where both sides put a penalty wide, it was Fishguard who soon went into the lead. Griffiths succeeded with his second penalty attempt to make it 3-0 before the fly-half crossed for the day's first try.
It was a superb individual effort, Griffiths jinking his way through the Wattstown defence and finishing with a swallow dive under the posts. The simple conversion was added and after 20 minutes, Griffiths had scored all of the Seagulls' points as they led 10-0.
Wattstown had struggled in the early exchanges, Ian Jones' penalty miss summing up their slow start. But after finding themselves 10-0 down, they started to grow into the game. A break from Mike Jenkins looked to have put him clear but the centre slipped on the Millennium Stadium turf and the chance was lost.
It was competitive stuff and with the contact area contested fiercely, it was no surprise to see referee Julian Smith lose patience with both sets of forwards. First Fishguard skipper Steven Jenkins was yellow carded before Wattstown's Brendon Lyons joined him soon after for a dangerous tackle.
And with 14 taking on 14, Wattstown finally responded with centre Lewis making the most of an overlap to score in the corner. The conversion was missed but when Jones dropped a goal right on the half time whistle, the Ducks trailed by just two at the break.
If Wattstown had finished the first half on a high, they started the second in similar fashion as two quick tries gave them control of the game. Gibbs finished in the corner and after returning from the bin, Lyons powered through some poor Fishguard tackling to dot down under the posts. Jones converted the second of those scores and after a slow start, Wattstown now led by 10.
Fishguard were now up against it and the task soon became stiffer when they were reduced to 13. Replacement prop Romeo Colella was yellow carded for being off his feet at a ruck and centre David Evans soon joined him on the sidelines.
With two men light, it seemed only a matter of time before Wattstown added a fourth try, replacement Bruford doing just that following a period of sustained pressure. Bruford converted his own score to make it 27-10 and give his side some breathing space.
And despite a late converted score from Fishguard's Bendall, Wattstown's lead proved enough for them to secure the trophy.