The influence of different types of humic substances (HS) is studied, in the presence or absence of calcium ions, on the retention of two triazines, atrazine and prometryn. To correlate the retention of triazines with the characteristic chemical parameters of the humic substances, three standard humic materials from the International Humic Substances Society (IHSS) as well as a NOM surrogate, tannic acid, are employed. Differences are observed, in the triazine retention behaviour, between organic-free triazine solutions and those of mixed HS–triazines. The results suggest that physicochemical interactions alone, between triazines and humic substances, cannot fully account for the observed triazine retention by nanofiltration. The HS acidity (total, carboxylic and phenolic) exhibits a weak correlation with triazine rejection. However, the conformation of humic species appears to play a more significant role. The presence of calcium ions improves both HS–triazine association and membrane rejection of the HS–triazine complexes. In support of the membrane filtration results, gel permeation chromatography shows that the hydrophobic interactions can explain the different triazine absorbing capacities of the HS used. In general, the results illustrate the complexity of the adsorption and retention mechanisms of triazines in the presence of humic substances, and confirm the important role of membrane fouling on process efficiency.