Grimsby's Central Library and Immingham Library have security between 16:30 and 19:45 BST, said Lincs Inspire.
Groups of 15 to 20 youths are meeting at the libraries and causing "nuisance and disturbance to regular users", the charity also said in a report.
The security measures are to be reviewed by 21 April, the charity said.
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Each library has one member of security staff in attendance, said the charity, which runs four libraries and five sporting facilities.
The security staff were recruited for Central Library on 30 January and at Immingham on 14 February.
The organisation said it was working with police and the council over anti-social behaviour and to provide safe libraries.
Humberside Police said it was carrying out regular patrols and would apply for Criminal Behaviour Orders to curb negative behaviour by repeat offenders.
The library problems are in a report to be discussed by North East Lincolnshire Council at a meeting on 12 April.
Two libraries have hired security staff after "unprecedented levels of disruption" by young people, according to the charity that runs them.