The use of seawater as the mix water has been thought to be inevitable for the near future as a result of increasing water scarcity. Hundreds of papers related to seawater mixed cement-based materials were published in recent years. Even though sulfate-resistant cement can be beneficial for internal sulfate attack and binding chloride ions, there is no related study on the sulfate-resistant cement together with seawater. In this study, the microstructure of seawater mixed sulfate-resistant pozzolanic cement was studied for the first time to understand possible reactions. Tap water and seawater mixes were designed by using Portland cement and sulfate-resistant cement with and without fibers. To examine the effect of seawater as the mix water on the microstructure quantitatively and to construct bridge between mechanical properties and microstructure, Rietveld refinements were performed on the obtained X-ray diffraction patterns. Thermogravimetric analyses were also carried out to correctly interpret and verify X-ray diffraction data. The possibility of internal sulfate attack, possible reactions and resulting hydration products were discussed. The results showed that internal sulfate attack is not a threat for seawater mixed concrete and sulfate-resistant cement can be a better alternative than portland cement owing to more chloride binding ability for seawater-mixed concretes.