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The sustainability of the Rawa Jombor Reservoir (RJR) in Indonesia is threatened by microplastic (MP) pollution. This issue requires critical investigation owing to possible detrimental consequences in humans, especially due to the growing concern regarding the adsorption of hazardous compounds by MPs. This study investigated the accumulation and characteristics of MPs in aquatic fauna (zooplankton, benthos, and fish), water samples, and sediments of the RJR, determined their interactions with heavy metals (HMs) (Cd, Cu, Zn, and Pb), and assessed their potential risk. The MPs extracted from aquatic fauna were characterized by stereomicroscopy, Fourier transform infrared spectroscopy (FTIR), scanning electron microscope energy-dispersive X-ray spectroscopy (SEM–EDS), and flame atomic absorption spectroscopy (FAAS). Their potential risk was assessed from the polymer hazard index (PHI), pollution load index (PLI), potential ecological risk index (PERI), estimated daily intake (EDI), target hazard quotient (THQ), total target hazard quotient (TTHQ), and target cancer risk (TR). MP concentrations were highest in the water near the main inlet (S1) and floating restaurant (S5), and the sediments near the densely populated water hyacinth area (S2). The pattern of MP accumulation in aquatic fauna, except the benthos, was similar to that of the MP concentrations in water. The MPs adsorbed high concentrations of HMs on their surface. MP concentrations in aquatic fauna increased through the food chains, indicating possible biomagnification. The fishes were safe for consumption, but their long-term consumption may induce cancer, primarily due to Cd. Therefore, the management of plastic waste by involving all stakeholders is crucial for mitigating this issue.