Large-aperture towed linear hydrophone array has been widely used for beamforming-based signal enhancement in passive sonar systems; however, its performance can drastically decrease due to the array distortion caused by rapid tactical maneuvers of the towed platform, oceanic currents, hydrodynamic effects, etc. In this paper, an enhanced data-driven shape array estimation scheme is provided in the passive underwater acoustic data, and a novel nonlinear outlier-robust particle filter (ORPF) method is proposed to acquire enhanced estimates of time delays in the presence of distorted hydrophone array. A conventional beamforming technique based on a hypothetical array is first used, and the detection of the narrow-band components is sequentially carried out so that the corresponding amplitudes and phases at these narrow-band components can be acquired. We convert the towed array estimation problem into a nonlinear discrete-time filtering problem with the joint estimates of amplitudes and time-delay differences, and then propose the ORPF method to acquire enhanced estimates of the time delays by exploiting the underlying properties of slowly changing time-delay differences across sensors. The proposed scheme fully exploits directional radiated noise targets as sources of opportunity for online array shape estimation, and thus it requires neither the number nor direction of sources to be known in advance. Both simulations and real experimental data show the effectiveness of the proposed method.