Numerical models with three-dimensional capabilities are necessary to accurately predict the propagation of anthropogenic noise in marine environments. This study validates the performance of a newly developed three-dimensional outward-only parabolic eq (3D PE) solver in dBSea version 3 against legacy two-dimensional numerical approximation (Nx2D) through comparison with empirical measurements. In situ acoustic measurements were collected in Tōtaranui, New Zealand. The study site features complex bathymetric data, with Motungārara Island creating an acoustic shadow zone, providing an ideal environment for validating 3D model performance. Field measurements were conducted using three autonomous recording units deployed over a 312-hour period, capturing Interislander ferry transits for direct and obstructed acoustic paths. The Nx2D solver demonstrated accuracy for unobstructed propagation paths at frequencies <630 Hz, but due to the two-dimensional treatment of propagation, it makes no prediction in the shadow zone. The 3D PE solver accurately reproduced measured sound levels within the shadow zone at frequencies ≤63 Hz, with modeled levels falling below the channel’s measured ambient noise floor at higher frequencies. Findings demonstrate the importance of three-dimensional modeling for environmental impact assessments in areas of strongly varying bathymetry where two-dimensional modeling may underestimate the potential impact of noise.