Organic matter in the water environment can enhance either flocculation or stabilization and, thus, controls the fate and transportation of cohesive sediments and causes seasonal variation in the turbidity of river water, determining floc morphology and settling velocity. The aim of this study was to elucidate the way that biological factors change the organic matter composition and enhances either flocculation or stabilization in different seasons. Jar test experiments were performed using a mixture of standard kaolinite and the filtered river water samples collected (bi-)weekly or monthly from April to December 2015 upstream a constructed weir in Nakdong River, to estimate the flocculation potential of the seasonal river water samples. Chlorophyll-a concentration, algae number concentration, and the fluorescence characteristics of organic matter were used to represent the biological factors. Our results revealed that flocculation potential depended not only on the algal population dynamics, but also the origins (or chemical composition) of organic matter in the river water. Extracellular polymeric substances (EPS), as algal organic matter, enhanced flocculation, while humic substances (HS), as terrestrial organic matter, enhanced stabilization, rather than flocculation. Since flocculation potential reached its maximum around the peaks of algal population, algae-produced EPS likely enhanced flocculation by binding sediment particles in the flocs. This observation supports previous findings of seasonal variation in EPS production and EPS-mediated flocculation. However, when HS was transported from the surrounding basin by a heavy rainfall event, cohesive sediments tended to be rather stabilized. Supplementary flocculation potential tests, which were performed with artificial water containing refined EPS and HS, also showed the opposing effects of EPS and HS.