Tunnel disease detection and maintenance are critical tasks in urban engineering, and are essential for the safety and stability of urban transportation systems. Water stain detection presents unique challenges due to its variable morphology and scale, which leads to insufficient multiscale contextual information extraction and boundary information loss in complex environments. To address these challenges, this paper proposes a method called Deep Aggregation Network with Edge Information Supplement (DAEiS-Net) for detecting tunnel water stains. The proposed method employs a classic encoder–decoder architecture. Specifically, in the encoder part, a Deep Aggregation Module (DAM) is introduced to enhance feature representation capabilities. Additionally, a Multiscale Cross-Attention Module (MCAM) is proposed to suppress noise in the shallow features and enhance the texture information of the high-level features. Moreover, an Edge Information Supplement Module (EISM) is designed to mitigate semantic gaps across different stages of feature extraction, improving the extraction of water stain edge information. Furthermore, a Sub-Pixel Module (SPM) is proposed to fuse features at various scales, enhancing edge feature representation. Finally, we introduce the Tunnel Water Stain Dataset (TWS), specifically designed for tunnel water stain segmentation. Experimental results on the TWS dataset demonstrate that DAEiS-Net achieves state-of-the-art performance in tunnel water stain segmentation.