Recently, seawater has emerged as viable mixing water for concrete, especially in the case of non-reinforced concrete applications or with the use of non-corrosive reinforcement. Previous studies concerning seawater-mixed concrete mostly revealed an initial slight increase in its strength performance (i.e., till Day 14 following mixing), followed by a strength reduction of 7–15% (i.e., after 28 days or longer) as compared to the conventional freshwater-mixed concrete. With an attempt to explain such observations, this paper aims at comparing the microstructure of freshwater- and seawater-mixed cement pastes. Scanning electron microscopy was utilized to observe the microstructure of freshwater and seawater pastes at Days 3 and 28 following mixing. At Day 3, seawater paste was observed to have more densified microstructure as compared to that of the freshwater counterpart, resulting in relatively higher strength performance. At Day 28, the microstructure was almost similar for the two cement pastes. However, seawater paste was observed to have salt impurities as a result of seawater ions, which possibly cause a slightly lower strength performance as compared to the freshwater paste.