Seawater can be used as mixing water for concrete with no steel reinforcement in some areas with difficult access to fresh water. Diatoms such as Phaeodactylum tricornutum are among the most abundant micro-organisms living in seawater, and they could be unavoidable when collecting seawater. In fact, diatoms can provide bio-SiO2 and bio-CaCO3 sources, namely amorphous nano-SiO2 and crystallised nano-CaCO3, which could be beneficial to cement hydration. Thus, the effects of different Phaeodactylum tricornutum concentrations (0%, 2.5% and 5% by weight of suspension of seawater and diatoms) in seawater on cement hydration in ordinary Portland cement (OPC) mixes (100% OPC) and ground granulated blast-furnace slag (GGBS) mixes (70% OPC + 30% GGBS) were investigated through tests of compressive strength, XRD, DTG–DTA and SEM. The results show that diatoms accelerated cement hydration by providing the nucleus for C-S-H structure and contributed pozzolanic reactions by amorphous nano-SiO2 and nano-CaCO3. The accelerated cement hydration was also confirmed by the fact that more Ca(OH)2 was formed in cement pastes with diatoms. However, it has also been found that diatoms decreased the compressive strength of cement pastes by leaving more weak bonds between the C-S-H structure, which was considered to be caused by the organic parts and the micron gap formed in diatoms. When comparing an OPC paste mix with 5% diatoms to a blank OPC paste, the reduction in compressive strength at 28 days can reach a maximum of 50.1%. The ability to provide bridging effects between C-S-H particles in GGBS paste was discovered to depend on the development of additional ettringite. This resulted in a 7.6% loss in compressive strength after 28 days in a GGBS paste with 5% diatoms.