The use of seawater to prepare geopolymers has attracted significant research attention; however, the ions in seawater considerably influence the properties of the resulting geopolymers. This study investigated the effects of magnesium salts and alkaline solutions on the microstructure and properties of ground-granulated-blast-furnace-slag-based geopolymers. The magnesium salt–free Na2SiO4-activatied geopolymer exhibited a much higher 28 d compressive strength (63.5 MPa) than the salt-free NaOH-activatied geopolymer (31.4 MPa), with the former mainly containing an amorphous phase (C-(A)-S-H gel) and the latter containing numerous crystals. MgCl2·6H2O addition prolonged the setting times and induced halite and Cl-hydrotalcite formation. Moreover, mercury intrusion porosimetry and scanning electron microscopy revealed that the Na2SiO4-activated geopolymer containing 8.5 wt% MgCl2·6H2O exhibited a higher critical pore size (1624 nm) and consequently, a lower 28 d compressive strength (30.1 MPa) and a more loosely bound geopolymer matrix than the salt-free geopolymer. In contrast, MgSO4 addition had less pronounced effects on the setting time, mineral phase, and morphology. The Na2SiO4-activated geopolymer with 9.0 wt% MgSO4 exhibited a compressive strength of 42.8 MPa, also lower than that of the salt-free geopolymer. The results indicate that Cl− is more harmful to the GGBFS-based geopolymer properties and microstructure than SO42− is.