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Microplastics, defined as plastic particles measuring less than 5 mm, are pervasive microscopic pollutants found in marine, estuarine, and freshwater environments globally. These pollutants pose significant threats to both the environment and marine life. The current prevalence of microplastics represents a critical issue for aquatic ecosystems. This study aims to develop a biofilter prototype designed to remove microplastics from water bodies. The methodology involves constructing a biofilter with two primary layers composed of dead coral skeletons with small pores, housed within PVC pipes, and utilizing a pump circulation system and reverse gravity to filter microplastic-laden water. This prototype is anticipated to effectively reduce microplastic content in water. To assess the reduction of microplastics, the study employs two main containers: the first containing 50 L of water sourced from public waters suspected of microplastic contamination, and the second serving as a receptacle for the filtered water. The filtration process is repeated three times, and microplastics in both containers are quantified using microscopic analysis. The findings indicate that the biofilter can remove approximately 70–80% of microplastics. From the results of the variance analysis, there was a significant difference between the number of microplastic particles before and after filtering. The study concludes that microplastic biofilters represent a promising solution for mitigating microplastic pollution in aquatic environments.