The current work scrutinizes the effectuation of seawater on morphological properties, pore structure, and compressive strength during the hydration process of fly ash blended cement at 3, 7, 28, 56, and 90 days to better understand the influence of salinity conditions of seawater on the microstructural modification and strength development of the hydration products as well as the total porosity. The chemical reaction's mechanism of mightily soluble salts, for example, MgSO and NaCl, with hydrated fly ash and blended cement (calcium-bearing phases) was also confirmed. Fourier-transform infrared spectroscopy has been appointed to observe and characterize the energetics of variation in the formulation of portlandite (CH), calcium silicate hydrate, gypsum (Gy), ettringite (AFt), and calcium chloroaluminate (Friedel's salt [FS]) throughout the hydration process of fly ash blended cement with seawater in comparison with deionized water. X-ray diffraction analysis exposed that the peak intensities of FS, portlandite, and some particular phases of the hydrated fly ash blended cement in seawater are higher and sharper than the comparable peaks in deionized water. Mercury intrusion porosimetry-measurements have been appointed that the total porosity of artificial seawater (ASW) was decreased from 28.9% at 3 days to 19.4% at 56 days. In addition, the average, median, and critical pore diameter were decreased in ASW while compared to deionized water (DIW). The reaction products of this work were also characterized using scanning electron microscopy, EDS, compressive strength, and isothermal calorimeter.