With the development of the marine economy, seawater is becoming more eutrophic. The risk of green tides from Enteromorpha is rising, which adversely affects the service of coastal infrastructure structures. To better evaluate the influence of algae on the long-term service performance of the structural concretes in coastal infrastructure, this study investigates the law of Enteromorpha-diatom attachment and growth on the mortar surface and its influence on the microstructure and durability of mortar. The results show that: 1) at 15 days, diatoms appeared on the surface of the mortar and biofilm appeared,the time period of adhesion and germination of Enteromorpha spores on the mortar surface was between 60 and 75 days. 2) Within 60 days, the spores released by the Enteromorpha preferentially germinate on the edges and in the pores of the mortar specimen, which can create micro-cracks on the mortar surface. Calcium carbonate may be involved in the metabolism of algae. 3) The pore size of the mortar surface gradually increases in the presence of bio-organic acids, which can accelerate the decrease of pH on mortar surfaces and reduce the resistance of mortar against chloride ions. This study confirms that green tide outbreaks may reduce the durability of cementitious materials, and provides a practical guide in the timing of protecting coastal infrastructure structures during the period of green tide outbreaks.