The objective of this work is to simulate a water-based flat plate photovoltaic/thermal system with glass cover and without it in laminar and turbulent regime and investigating the effects of solar irradiation, packing factor, Reynolds number, collector length, pipes diameter and number of pipes on the performance of this system. The accuracy of the model has been validated with the available data in the literature, where good agreements between the results have been achieved. The results showed that the energy efficiency in the glazed photovoltaic/thermal system is higher than unglazed one, while its exergy efficiency depends on the packing factor, Reynolds number and collector length. The results also indicated that increasing of solar radiation and packing factor increases total energy and exergy efficiency in both laminar and turbulent regime. Besides, it was found that there are the optimum values for mass flow rate and number of pipes that maximize exergy efficiency. The value of the optimum mass flow rate is larger in the case of unglazed system compared to that of glazed one. Furthermore, in most cases, the total energy efficiency in turbulent regime is higher, whereas the total exergy efficiency in laminar regime is superior. (C) 2016 Elsevier Ltd. All rights reserved.