The former manager believes the club should be more focused on maintaining their Premier League status.
Qualifying for Europe was deemed a successful campaign for the Saints after a summer which saw them sell off most of their top talent, with the likes of Luke Shaw, Adam Lallana, Dejan Lovren and Calum Chambers all leaving the club in big money moves.
Instead, the Saints flourished under new manager Ronald Koeman and were at one point challenging for a Champions League place.
They eventually qualified for the Europa League, and Souness believes there is nothing positive about that, having experienced the trouble it can cause when in charge of Blackburn.
“I think that it might be a problem,” Souness said.
“You’re playing catch up when you come back, you’re playing on a Sunday all the time. The pressure is on you if the teams around you have won on the Saturday. That will, unfortunately, impact of Southampton next season.”
It’s a well held belief in England that the Europa League negatively affects league performances, with Everton last season seemingly suffering from their European exploits.
The Blues' league form suffered heavily when they were still in the competition but seemingly picked up once they were knocked out. And Souness believes for clubs like Southampton, maintaining their status in the league is more important.
“Your eyes are taken off the bigger picture,” he added.
“The bigger picture for clubs like Southampton is maintaining your Premier League status. That’s how the club moves forward.”