This study aimed to check how herbicide 2,4-dichlorophenoxyacetic acid (2,4-D) affects the production of EPS and its composition, growth, and biomass, as well as morphology in a cyanobacterial species isolated from a rice field in Meghalaya, India. Compared to the control cells, the growth of the organism measured in terms of chlorophyll concentration increased after being exposed to 10 and 20 ppm 2,4-D. However, cultures treated with 30 and 40 ppm experienced a decrease in their growth. Likewise, the biomass content of the organism experienced a minuscule increase in content upon exposure to 10 and 20 ppm 2,4-D but was compromised upon exposure to higher doses. When exposed to 10 ppm, the total EPS content, which includes the RPS and CPS content, showed a substantial increase. Maximum EPS production was seen at 20 ppm 2,4-D. However, exposure to 30 and 40 ppm 2,4-D, EPS production in the organism experienced a significant reduction, respectively. All components of EPS, such as uronic acid, neutral sugar, and proteins, individually showed an increase in 10 and 20 ppm 2, 4-D. A similar trend was seen in the organism’s bio-flocculating activity, which increased when exposed to 10 and 20 ppm, respectively. However, this activity in cells exposed to 30 and 40 ppm 2,4-D was severely reduced. Not only the content of EPS but the rate of EPS production was also enhanced in lower concentrations of 2,4-D. Although exposure to 30 ppm 2,4-D, the rate of EPS production was not significantly compromised, 40 ppm exposure adversely affected the rate of EPS production. Furthermore, visualization using scanning electron microscopy revealed the morphological changes induced by the herbicide 2,4-D.