Transitional ecosystems, such as estuaries, are among the most susceptible regions to plastic pollution. The objective of this project is determining the occurrence and spatial distribution of Microplastics (MPs) and the presence of litter windrows as potential hotspots of MPs on the water surface of a subtropical estuarine complex. In 2022, 14 surface water (< 0.20 m) samples were collected with a trawl net called NOIVA. Each trawl was carried out at a speed of 5 km/h, for 5 min, always on the neap tide, along the Paranaguá Estuary Complex (PEC). In the laboratory the samples were sieved through 1 mm stainless steel mesh. The items were visually inspected through a stereomicroscope to select potential microplastics. The hot needle test and attenuated total reflectance Fourier transform infrared was applied to confirm the composition of items. Statistical analyses were performed (PERMANOVA and CAP). A total of 40 MPs were found in all sectors. Fragments are the most frequent (70%). Secondary MPs represented 95% of the items, among which the most common are 3–4 mm large (35%) and white (27.5%) particles. Polypropylene (PP) was the most common type (42.5%). The average concentration of MPs in the PEC (0.149 ± 0.37 mp/m3) is comparable to that found in other estuaries. Estuarine litter windrows (ELWs) play an important role in the accumulation of floating MPs in the PEC (1.42 mp/m3). The omnipresence of MPs at a World Heritage Site is alarming. There is an urgent demand for pollution control, especially regarding adequate waste management strategies to reduce the presence of marine litter.