Intraplate deformation, influenced by tectonic, geological, and environmental factors, presents significant challenges for geodesy and geodynamics. This study focuses on quantifying intraplate deformation within the Nubian Plate using residual velocity fields derived from two GPS-based velocity models, MIDAS and HECTOR, referenced to the ITRF2014 frame. This research analyzes 20 years of daily GPS coordinate time series (2000–2021) from 25 continuously operating stations across West Africa, offering a detailed regional perspective. The primary objectives include generating outlier-free coordinate time series from station daily geocentric coordinate data, evaluating noise characteristics using spectral analysis to assess station stability, and modeling horizontal and vertical deformation patterns using residual velocity analysis. An examination of the noise patterns in the GPS coordinate time series data revealed flicker noise to be the dominant type, confirming the fairly stability of GPS stations for precise geodetic measurements. Horizontal deformation rates were found to range from 0 to 2.0 mm/yr, while vertical rates varied between −1.3 and 3.0 mm/yr, indicating localized subsidence and uplift influenced by tectonics, sediment loading, and groundwater extraction. Both MIDAS and HECTOR models captured consistent deformation patterns with an average deformation rate of 0.8 mm/yr in all coordinate components but revealed marginal regional discrepancies, reflecting differences in velocity modeling approaches. Residual velocity statistics indicate greater variability in horizontal deformation with a standard deviation of 1.6 mm/yr compared to vertical deformation with a standard deviation of 0.9 mm/yr. The larger horizontal standard deviations, 1.7 times greater than the vertical, may be due to the simultaneous use of ITRF- and GPS-based velocities to estimate the residual velocities, unlike the vertical component, which relies solely on GPS data. This study highlights the importance of integrating localized deformation data into geodetic infrastructure designs, advocating for GPS upgrades and advanced processing to improve measurement precision, enhance hazard assessments, and support resilient infrastructure development in West Africa.