A statistical investigation is performed into the effectiveness of two disinfectants (gaseous ClO2 and weak acid hypochlorous water) in improving the indoor air quality in the reading room and study carrels of a university library in Taiwan. For each disinfectant, three different treatment modes are considered, namely a single-daily disinfection mode (SM), a twice-daily disinfection mode (TM), and a regular disinfection mode (RM). The results show that both disinfectants reduce the bacteria and fungi concentrations within the experimental areas. For the study carrel, with a relatively small and confined area, the weak acid hypochlorous water twice-daily disinfection mode (WTM) outperforms the ClO2 twice-daily disinfection mode (CTM). In the reading room, no significant difference is observed in the disinfection performance of the two disinfectants due to the large and semi-closed nature of the room. An extreme negative correlation is found among the airflow velocity, the residual bacteria and fungi concentrations. Hence, it is inferred that a higher air velocity is beneficial in spreading the disinfectant within the indoor space and improving the disinfection efficiency as a result.