In practical work scenarios, it is common for multiple vessels to be present in close proximity within the same water area. In such cases, the acoustic signals emitted by these vessels often overlap, causing interference and reducing the accuracy of vessel identification. This paper proposes an improved GALR end-to-end underwater acoustic source separation algorithm, with ECA-DE (Efficient Channel Attention-Deep Encoder) and Bi-GRU (Bidirectional Gated Recurrent Unit), which consists of an encoder, separation blocks, and a decoder (EDBG-GALR). Addressing the issue of GALR encoder’s limited expressiveness due to its single-layer one-dimensional convolutional layer, we introduce a new deep encoder, ECA-DE, to enhance the encoder’s capability to process temporal signals and improve the efficiency of the separator’s input. Additionally, we integrate Bi-GRU into the GALR separation block’s local modeling module to enhance the local modeling ability of sequence features, thereby reducing the model’s computational and parameter requirements. Experimental results demonstrate that the proposed EDBG-GALR method can effectively separate mixed multi-target signals into multiple single-target signals, achieving a maximum scale-invariant signal-to-noise ratio (SI-SNR) improvement of 3.32 dB and a signal distortion ratio (SDR) improvement of 3.38 dB over baseline methods. These results highlight the practical applicability of EDBG-GALR in complex underwater environments.