The coupling of low-frequency oscillatory modes of a harbor with horizontal motions of moored ships can amplify the latter, causing operational and safety problems. The objectives of this study were to analyze infragravity waves and their effect on moored ship motions; to validate the Wavelet Transform Analysis (WTA) method for studying port-ship resonance in the Outer Port of Punta Langosteira, Spain; and to study the climatic forcing of downtimes. The excited resonant modes of the basin (102 and 132 s) were determined using a numerical model and high-frequency water level measurements at different points of the harbor. Yaw and sway motions of three bulk carriers were analyzed in the frequency-time domain using WTA. The results showed that the oscillation periods of the studied vessel motions are directly related to the water depth to vessel draft ratio. In addition, when the wind speeds exceeds 20 km/h, the ship moves away from the fenders, which lead to a lengthening of these periods. Based on our findings, yaw may induce oscillations of the same period in sway. Additionally, operational thresholds were proposed based on outer and inner waves data that will lead to optimize ship stays, avoiding downtimes, and to advance the safety of loading and unloading operations.