Seawater treated with lime and sodium carbonate in different proportions to reduce magnesium and calcium contents is used in flocculation and sedimentation tests of artificial quartz and kaolin tailings. Solid complexes were separated from water by vacuum filtration, and factors such as lime/sodium carbonate ratio, kaolin content, flocculation time, and flocculant dose are evaluated. The growth of the aggregates was captured in situ by a focused beam reflectance measurement (FBRM) probe. Solid magnesium and calcium complexes are formed in raw seawater at pH 11, impairing the performance of flocculant polymers based on polyacrylamides. The results show that the settling rate improved when the treatment’s lime/sodium carbonate ratio increased. That is, when a greater removal of magnesium is prioritized over calcium. The amount of magnesium required to be removed depends on the mineralogy of the system: more clay will require more significant removal of magnesium. These results respond to the structural changes of the flocs, achieving that the more magnesium is removed, the greater the size and density of the aggregates. In contrast, calcium removal does not significantly influence flocculant performance. The study suggests the necessary conditions for each type of tailing to maximize water recovery, contributing to the effective closure of the water cycle in processes that use seawater with magnesium control.