Due to their high durability and immobilization properties, cementitious materials have found a considerable application in the design and construction of radioactive waste repositories in the last decades. During cement paste production, organic additives are introduced to modify various properties of cement. The presence of such organic complexants may negatively affect the immobilizing properties of cement with respect to radionuclides. For better understanding and prediction of the effects of interactions between organic molecules and cementitious materials with radionuclides, we have developed several representative models consisting of three principal components: (i) calcium silicate hydrate (C–S–H) phase - the main binding phase of cement; (ii) gluconate, a simple well-described molecule, as a representative of organic additives; (iii) U(VI), as one of the most studied radionuclides of the actinide series. The C–S–H phase with low Ca/Si ratio (~0.83) typical for “low-pH” and degraded cement pastes has been selected for this modelling study. Structural, and energetic aspects of the sorption processes of uranyl, gluconate, and their mutual correlations on the surface of cement were quantitatively modeled by classical molecular dynamics (MD) and potential of mean force (PMF) calculations. The ternary surface complex formation between uranyl hydroxides and Ca2+ cations at the C–S–H aqueous interfaces is shown to have an important role in the overall sorption process. In the presence of gluconate, U(VI) sorption on C–S–H is facilitated by weakening the Ca2+ binding with the surface. Additionally, Na+ is proven to be an important competitor for certain surface sorption sites and can potentially affect the equilibrium properties of the interface.