This study investigates basin, basin edge and complex topography effects in ground motion records using residuals from empirical ground motion models, to better understand regional site amplification patterns in Türkiye. Using data from the updated Strong Motion Database of Türkiye (SMD-TR) strong-motion database, we compute residuals using site amplification function and analyze their spatial distribution across regions. The clustering technique, Gaussian Mixture Models (GMM), is employed to identify regions with coherent residual patterns, primarily to capture regional site effects. After regionalization, peak amplifications within the VS30 range of 400–550 m/s are examined for potential associations with sedimentary basins or basin edge effects. The results reveal systematic amplification anomalies within the VS30 range of 400–550 m/s that are not fully captured by conventional site proxies such as VS30. Notably, residuals consistently cluster along basin edges and within deep valley regions, indicating the influence of complex three-dimensional and topographic amplification mechanisms. These observations underscore the limitations of current site characterization approaches and motivate further refinement of site response models, particularly for partially non-ergodic applications in seismic hazard analysis. This study focuses on residual-based evaluations to identify potential basin, basin-edge, and topographic effects that warrant more detailed investigation.