Long–term ambient vibration monitoring campaigns show that environmental parameters (such as temperature, humidity, wind speed and direction) can influence the structures' static and dynamic behaviour. In particular, thermal variations can affect the modal characteristics of ancient masonry constructions. This work presents a procedure combining experimental and numerical steps to monitor, assess and model the dynamic behaviour of masonry structures subjected to thermal loads. The procedure is tested and validated through two numerical examples and the simulation of a full-scale masonry structure, the Mogadouro clock tower in Portugal, monitored with accelerometers and temperature and humidity sensors.