For the past decades, the ubiquity of plastic pollution has raised the concern of all layers of the society towards the consequences of this synthetic material in the environment. However, the focus of the scientific community concerning plastic pollution has mainly turned to marine environments, while other environments have been disregarded. Estuaries are particularly pressured by polluting human activities. Aquacultures are among the main activities in estuaries and are quickly expanding, to match the market demand for alternatives to capture fisheries. Fish production is particularly important in Southern European countries, and in some, as Portugal, fish are reared in semi-intensive regimes, using estuarine water for the rearing tanks. The water is kept in the tanks roughly two weeks, after which it is released to the estuary, while water with lower matter load is brought in. Due to the worldwide importance of fish as a food source and given the particularities of semi-intensive practices, there is an interest in understanding the pressure of plastic pollution in these systems. Thus, the present study aims to understand the path of plastic input in estuaries, particularly in aquacultures. Therefore, water, sediment and fish were sampled from four Portuguese aquacultures, located in two estuaries – Mondego and Sado –, subjected to different polluting pressures. Results show i) water released from the rearing tanks carries higher microplastic load, compared to incoming water; ii) water from the Sado estuary, which supports more human activities compared to the Mondego estuary, presents a higher count of microplastic particles; iii) sediments enclose microplastics of higher density, that sink due to low water dynamics; iv) fish tissue accumulates different types of microplastics. This study provides further supporting material to enhance strategies to food safety and security and to the economic development, highlighting the potential impacts to human diet and health.