Historical and cultural heritage must be preserved and protected from deterioration. In particular, the integrity of structures is threatened by inadequate maintenance, exceptional events (such as fires and floods), and exposure to increasing air pollution. In addition, indoor environments may provide favorable conditions for colonizing harmful agents. Fungal contamination and growth in buildings can lead to the deterioration of surfaces. Fungi need damp environments to germinate and grow, for example, in the presence of water condensation on surfaces. In this paper, an investigation is carried out to examine the conditions that favor the growth of different fungal species on building materials commonly used in historic buildings, such as brick masonry, limestone, and plaster. The analyzed climatic conditions refer to three locations, typical of Northern, Central, and Southern Europe, respectively. These conditions are obtained using the DesignBuilder software. A more detailed analysis of the walls is then performed with the WUFI software. The paper suggests solutions to reduce the risk of fungal growth and, therefore, to avoid phenomena that can damage the historical heritage.