A method and system of compensating for environmental effect when detecting signals using a structural health monitoring system includes collecting baseline data signals for one or more values of the environmental effect variable from signals transmitted along selected paths between transducers in an array attached to the structure. A threshold is selected based on the baseline data for determining if the signal is detected. Current data signals are collected and matched to the best fit baseline data. The value of the environmental effect variable is determined on the basis of the matching. A signal is detected according to the selected threshold.