Strategically important objects, such as dams, tunnels, bridges, and others, require long-term structural health monitoring programs in order to preserve their structural integrity with minimal downtime, financial expenses, and increased safety for civilians. The current study focuses on developing a damage detection methodology that is applicable to the long-term monitoring of such structures. It is based on the identification of resonant frequencies from operational modal analysis, removing the effect of environmental factors on the resonant frequencies through support vector regression with optimized hyperparameters and, finally, classifying the global structural state as either healthy or damaged, utilizing the Mahalanobis distance. The novelty lies in two additional steps that supplement this procedure, namely, the nonlinear estimation of the relative effects of various environmental factors, such as temperature, humidity, and ambient loads on the resonant frequencies, and the selection of the most informative resonant frequency features using a non-parametric neighborhood component analysis algorithm. This methodology is validated on a wooden two-story truss structure with different artificial structural modifications that simulate damage in a non-destructive manner. It is found that, firstly, out of all environmental factors, temperature has a dominating decreasing effect on resonance frequencies, followed by humidity, wind speed, and precipitation. Secondly, the selection of only a handful of the most informative resonance frequency features not only reduces the feature space, but also increases the classification performance, albeit with a trade-off between false alarms and missed damage detection. The proposed approach effectively minimizes false alarms and ensures consistent damage detection under varying environmental conditions, offering tangible benefits for long-term SHM applications. © 2025 by the authors.