This study investigates the impact of hydrological mass loading on the Egyptian Permanent GNSS Network (EPGN) stations. Initially, GRACE and GRACE-FO products are evaluated, resulting in selecting the CSR center’s DDK5 monthly solutions for estimating terrestrial total water storage (TWS) in terms of equivalent water height (EWH). Monthly vertical displacements (VD) rates are calculated using GNSS data from EPGN stations, while TWS in terms of EWH is derived from GRACE/GRACE-FO data and WGHM model at the same locations. The fndings from GRACE show that the mean monthly EWH values exhibit a negative trend of − 2.36 mm/year from 2002 to 2012, followed by a positive trend of 3.94 mm/year from early 2013 until mid-2017. For GRACE-FO solutions, EWH shows a positive trend of 5.69 mm/year from mid-2018 to early 2024. A comparison of mean monthly EWH variations from GRACE/GRACE-FO and WGHM with GNSS derived VD demonstrates a negative correlation at most GNSS stations, particularly in areas with signifcant hydrological signals, such as the Egyptian Delta and Lake Nasser. This emphasizes the impact of hydrological mass changes on these stations. Finally, mean monthly EWHs from GRACE are evaluated against the WGHM over Egypt. In addition, water level heights are compared to the EWHs from GRACE and WGHM at the ABSM station near Lake Nasser. Results show good agreement between EWHs estimated from GRACE and the WGHM over Egypt. At ABSM station, the water level heights of Lake Nasser provide robustness of our fndings.