The Dutch midfielder spent last season at the Liberty Stadium and scored eight goals as the Swans finished ninth in the Premier League.
Chairman Huw Jenkins said that the 25-year-old would review his long-term future at the end of the upcoming campaign.
"Everyone is happy the loan is continuing," Jenkins told the club's website. "Then Jonathan will review his long-term future next summer."
Swansea begin their 2013-14 campaign in difficult fashion, hosting defending champions Manchester United in South Wales.