Ship noise recorded by a vertical hydrophone array in the Mississippi Canyon region of the Gulf of Mexico is shown to contain the acoustic influence of bathymetric features, seabed properties, and water column sound speeds. Noise coherence is demonstrated to be an effective metric not just for identifying ship traffic in recorded data but also for "fingerprinting" the environment. A three-dimensional acoustics model adopting automatic identification system ship track information and realistic oceanographic conditions is used to compute noise coherence distributions across the canyon area and enables numerical study of the water column sound speed effects that can lead to temporal changes in noise coherence. The study shows the importance of including in situ sound speed measurements or constraints in passive ship noise localization from coherence measurements. Seasonal variability is also examined with models suggesting a strong influence of seasonal changes.