This paper deals with the evolution monitoring of biomass colonization and mechanical properties of 3D printed eco-materials/mortars immersed in the sea. Measurements of tensile strength, compressive strength, and Young’s modulus were determined on samples deployed along the Atlantic coast of Europe, in France, United Kingdom, Spain, and Portugal. The samples were manufactured using 3D printing, where six mix designs with a low environmental impact binder were used. These mortars were based on geopolymer and cementitious binders (Cement CEM III), in which sand is replaced by three types of recycled sand, including glass, seashell, and limestone by 30%, 50%, and 100% respectively. The colonization of concrete samples by micro/macro-organisms and their durability were also evaluated after 1, 3, 6, 12, and 24 months of immersion. The results showed that both biomass colonization and mechanical properties were better with CEM III compared to geopolymer-based compositions. Therefore, the mixed design optimized according to mechanical properties show that the use of CEM III should be preferred over these geopolymer binders in 3D printed concrete for artificial reef applications.