Deepfake technology poses increasing risks such as privacy invasion and identity theft. To address these threats, we propose WaveGuard, a proactive watermarking framework that enhances robustness and imperceptibility via frequency-domain embedding and graph-based structural consistency. Specifically, we embed watermarks into high-frequency sub-bands using Dual-Tree Complex Wavelet Transform (DT-CWT) and employ a Structural Consistency Graph Neural Network (SC-GNN) to preserve visual quality. We also design an attention module to refine embedding precision. Experimental results on face swap and reenactment tasks demonstrate that WaveGuard outperforms state-of-the-art methods in both robustness and visual quality. Code is available at https://github.com/vpsg-research/WaveGuard.