The Spaniard started the season opener at Derby on Sunday but had to be substituted in the first half after falling awkwardly.
Bowyer confirmed today that the 22-year-old would undergo surgery on Wednesday.
"I think we are talking months [out] rather than weeks," Bowyer told the club website. "It could be three months, but we have a top class medical team so we'll see."
gracias por el apoyo mostrado en las ultimas horas! // thanks for the support you shown me in the last few hours! pic.twitter.com/pHuTDySfw3— Ruben Rochina Naixes (@rubenrochina23) August 4, 2013
Blackburn's next match is a trip to Carlisle United in the first round of the Capital One Cup tomorrow.