Before settling into adult benthic or pelagic habitats, fish spend their larval phase in the meroplankton. Like the rest of the zooplanktonic organisms, they are at the base of the food web and can therefore act as entry points for pollutants. Anthropogenic particles (APs), including microplastics, are ubiquitous and can bioaccumulate and biomagnify, causing adverse physiological effects on this fragile life stage and higher trophic levels. In this study, we investigated the ingestion of APs in wild fish larvae from two coastal ecosystems of the southern Portuguese Coast: the Guadiana River estuary and the Ria Formosa lagoon, sampled between April 2023 and March 2024. Of the 129 larvae, belonging to six different families and one order: Gobiidae (57.4%), Atherinidae (14.7%), Sparidae (13.2%), Blenniidae (6.2%), Clupeiformes (2.3%), Soleidae (1.6%) and Labridae (0.8%), a total of 16 particles were recovered, classified and then analysed using a μ-FTIR. The particles ranged from 20 μm to 2 mm; they were mainly fibres, transparent and made of rayon. The Encounter Rate (ER = [Total ingested particles / Total organisms analyzed] 100) varied between 0% and 66.7% across taxa, though no statistically significant differences were observed between taxonomic groups or sampling locations. Consistent with findings across other European coastal waters, these results confirm that fish larvae actively ingest particles of anthropogenic origin in natural habitats. This highlights the critical role of nursery grounds as microplastic exposure hotspots.