Environmental and operational variations present a significant challenge in the long-term health monitoring of bridge structures due to their potential to cause serious confounding influences and wrong decisions. These influences may lead to false alarms of damage during normal operation of a civil structure or, conversely, mask actual damage, resulting in a failure to correctly signal a warning. Consequently, a critical task in structural health monitoring, particularly for bridges, is to mitigate the negative impact of environmental variability. An initial approach is to measure the most influential environmental and operational factors and then apply statistical tools to eliminate their effects. However, this approach may not be effective under all conditions. Therefore, the primary objective of this paper is to propose an innovative unsupervised statistical learning method that addresses the challenges posed by environmental and operational variability by considering unmeasured factors. The proposed method involves three steps: data clustering, unsupervised feature selection, and novelty detection. The initial step utilizes k-means clustering to categorize features (modal frequencies) into five types of clusters, reflecting the influence of five environmental and operational factors on bridge structures; that is, temperature, humidity/rain/snow, wind speed/direction, traffic, and damage. These clustered features are then processed through an unsupervised feature selection algorithm based on reconstruction independent component analysis to extract new features. These reduced features are subsequently employed in a novelty detection model, developed using the Mahalanobis-squared distance, to analyze the environmental and operational effects. Real dynamic data of a steel arch bridge is utilized to verify the proposed method. Results demonstrate that this method can effectively handle the demanding issue stemming from unmeasured environmental and operational variability conditions.