Microplastics are widely used to manufacture diverse products such as textiles, skin care products, and household products such as detergents and soaps. However, microplastic pollution and its potential health risks are raising concerns worldwide. This study characterized and determined the safety of microplastics in water and sediments obtained from three locations, namely Ibeshe, Amuwo Odofin, and Ojo along Badagry lagoon, Lagos, Nigeria. The samples of the lagoon's surface water and sediments were treated and analyzed for the abundance of microplastics, as well as their shapes, sizes, and types of polymers. The risk index of the polymers in the microplastics was also estimated. Microplastics were found to be more abundant (p ≤ 0.05) in the sediments (283–315 particles/kg) than in the surface water (108–199 particles/L). In both the water and sediments at all the locations, the dominant shapes were fibers (52%–90%), followed by fragments (3%–32%) and films (1%–25%). In order of significance, the microplastic size range of 0-100µm and 100-500µm dominated the surface water, while the size range of 1000-5000µm and 500-1000µm dominated the sediments at all the locations. The dominant polymers in both the water and sediments at all the locations were polyethylene, polypropylene, and polyamide, while the least was polystyrene. In both the water and sediments at all the locations, the dominant risk score among the polymers is III (moderate risk). The results obtained suggest that microplastic pollution poses environmental and health risks to the lagoon, aquatic organisms, and humans. As such, the lagoon required microplastic remediation and control.