Understanding the spatial and temporal distribution of small water bodies is essential for managing water resources, crafting conservation policies, and preserving watershed ecosystems and biodiversity. However, existing studies often rely on a single remote sensing data source (optical or microwave), focusing on large-scale, flat areas and lacking comprehensive monitoring of small water bodies in complex terrain. Therefore, considering the complementary advantages of multisource remote sensing (multispectral and SAR), this paper proposes a multispectral and SAR fusion algorithm, named Multispectral and SAR Fusion algorithm (MASF), to better capture the remote sensing characteristics of small water bodies in complex areas. Based on this, a dataset containing spectral, texture, and geometric features is constructed, and multi-scale segmentation and random forest algorithms are applied for identification of small water bodies in complex terrain. The results demonstrate that the proposed fusion algorithm MASF exhibits minimal spectral distortion (SAM < 3.5, ERGAS <21, RMSE <0.01) and robust spatial feature enhancement (PSNR >40, SSIM >0.999, CC > 0.99). The Overall Accuracy (OA) and Kappa coefficients for both experimental areas surpassed 0.9. For rivers and reservoirs, both Producer's Accuracy (PA) and User's Accuracy (UA) exceeded 0.9. The UA for agricultural ponds exceeded 0.8. Comparative analysis with three other types of water-related data products shows that the freshwater identification results in this study have certain advantages in local small water bodies. Our research holds significant implications for the utilization of water resources in mountainous areas, prevention and control of floods and floods, as well as the development of aquaculture industry.