This study investigates the data normalisation of modal parameters of an operating concrete–steel hybrid onshore wind turbine tower considering also the identification uncertainty. In order to take into account the Environmental and Operational Condition (EOC)-dependent variance, sparse heteroscedastic Gaussian processes (GPs) are used for the data normalisation. Following a typical vibration-based Structural Health Monitoring (SHM) scheme, data normalisation of the natural frequencies and the mode shapes is performed first. Subsequently, a metric is defined which takes into account both the identification uncertainty and the operation-dependent uncertainty in order to enable novelty detection. The data normalisation methods must be able to handle uncertainties of different magnitudes due to EOCs in the data. In this context, GPs can be a suitable tool. However, standard GPs assume homoscedasticity, which is an unrealistic assumption in the case of EOC-dependent variance. Using a heteroscedastic GP instead, the variance of the data is better mapped and allows comparison with the identification uncertainties of Bayesian operational modal analysis (BAYOMA), taking into account the specifics of closely spaced modes of the tower structure. This leads to a better interpretation of the data and enables the introduction of a probabilistic novelty metric. This data normalisation approach, taking into account EOC-dependent uncertainties using heteroscedastic GPs, is being applied for the first time to a tower of a full scale 3.4 MW wind turbine in operation. Following this approach, it is possible to detect smaller changes in natural frequencies and second-order modal assurance criterion (S2MAC) compared to the assumption of homoscedasticity within the GP. In addition, a novelty was detected using the S2MAC during the period under study. Therefore, it can be illustrated that mode shape-based metrics tend to be more sensitive than purely frequency-based ones. However, it is difficult to assess the significance of such changes for structural integrity without further information.