Holothuria atra (Echinodermata: Holothuroidea) is a type of invertebrate animal that lives on the bottom of the rocky coast and has the potential as a nutritious food raw material for humans and pharmaceutical raw materials. The study aims to determine the microplastic types, microplastic functional groups and simulate the distribution pattern of ingested microplastics in the digestive system of H. atra based on hydrodynamic activity. Microplastic separation was conducted by extraction using the flotation method based on predetermined criteria. Functional group test of microplastic polymers ingested in intestines of sea cucumbers using FT‐IR (Frontier Transform Infrared‐Spectroscopy) Analysis. Hydrodynamic modeling analysis used secondary data: bathymetric, currents, wind direction, and tidal prediction data. The results of sampling of H. atra sea cucumbers at four observation locations, where ten individual sea cucumbers were taken from each location, showed that microplastic waste exposed in the intestines of sea cucumbers obtained an average value of 14,166 individuals‐1, with a particle length range of 0.214–3.978 mm. The highest abundance was from the type of fiber, followed by fragments, pellets, and films. FTIR test results indicate the presence of several functional microplastic groups that are digested in the intestine, including polyamide (PA)/nylon‐6, polyethylene (PE), polypropylene (PP), and polystyrene (PS). The movement of currents carrying microplastic waste particles is dominated to the west and south of Karimunjawa Island, potentially endangering the habitats of sea cucumbers and other animals in the waters of the surrounding small islands. It is recommended that stakeholders establish plastic waste protocols, waste facilities and treatment, and strict supervision of tourists entering the Karimunjawa tourism environment.