We have monitored the presence of bacteria belonging to the genus Legionella in the plumbing of buildings at the University of Perugia (Italy). More than 300 water samples were collected from 156 control-point taps in 41 buildings comprised in the eight campuses of the University. Legionella was absent in most samples, while it was found in only 12 buildings (29% of the total). Molecular analysis indicated the presence of L. pneumophila (serogroups 1, 8 and 6–10), L. taurinensis and L. anisa. In only three cases contamination levels were above the limit at which remedial actions are required, according to international guidelines. In two buildings, where the water temperature could be raised and maintained above 60 °C, thermal disinfection was effective in eradicating Legionella. Conversely, in buildings where contaminations were caused by heat exchangers that produced hot water at a maximum temperature of 50 °C, a chemical disinfection with silver hydrogen peroxide was carried out but was effective only in the short term. In this case study, Legionella contaminations and remediation effectiveness strongly depended on the network and heating-system characteristics, indicating how a multidisciplinary approach that integrates microbiological analysis with hydraulic surveys is necessary for an effective definition of Legionella prevention and control strategies.