Bubbles in submarine cold-seep plumes cause strong scattering, attenuation, and poor continuity in water-column seismic responses, hindering continuous two-dimensional characterization of acoustic properties. Using multichannel seismic data from the Shenhu area, northern South China Sea, this study proposes a conductivity–temperature–depth (CTD)-constrained, layer-wise two-angle allied elastic impedance (AEI) inversion method to reconstruct water-column velocity. Based on the scattering-equivalent AEI theory, a two-angle equation is derived for layer-wise estimation of water-column velocity, thereby providing a theoretical basis for the subsequent inversion. A relative-amplitude-preserving workflow mitigates bubble-induced attenuation and random scattering, while pre-stack time migration produces common reflection point (CRP) angle gathers. Coherent scattered energy after imaging is parameterized by the local scattering half-angle. Small-angle and large-angle gathers are selected according to effective angular coverage for AEI inversion. CTD-derived seawater velocity and density provide AEI constraints, and the normalized two-angle AEI equation yields a continuous velocity section. Results show velocities of 1460–1560 m/s, with pronounced vertical stratification, relatively weak lateral variation, and agreement between inverted and CTD-derived velocity trends. Within the 0–1800 ms water-column time window, the root-mean-square difference between the inverted and CTD-derived velocities is 18.19 m/s. Combining the lateral continuity of multichannel seismic data with high-accuracy CTD-derived physical-property constraints enables continuous two-dimensional velocity reconstruction in bubble-scattering water columns and offers a new approach for observing cold-seep velocity structure and geophysically characterizing bubble-plume activity.