Accuracy and resolution are the two primary challenges that impose limitations on the practical implementation of classical tide-level remote sensing. To improve the accuracy and applicability and increase the temporal resolution of the inversion point near the shore area, the influence of coastal reflection signals in the signal-to-noise ratio (SNR) residual sequence should be weakened significantly. This contribution proposes an anti-interference GNSS Multipath Reflectometry (GNSS-MR) algorithm called VMD_SNR, which is enhanced using variational mode decomposition (VMD). Compared with wavelet decomposition and empirical mode decomposition (EMD) methods, VMD_SNR exhibits superior capabilities in reducing the interference caused by noisy signals. The measurements of ground-based GNSS stations are used to verify the performance improvement in the VMD_SNR algorithm. The results show that the proposed algorithm is better than the wavelet decomposition method and EMD method in terms of accuracy and stability in the shore area, where the effective number is higher than 99% of the total number, and the accuracy is better than 13.80 cm. Moreover, the accuracy improvement is more significant in the high-elevation range, which is 30.16% higher than the wavelet decomposition method and 38.34% higher than the EMD method.