Nematodes are essential contributors to soil food web, playing a crucial role in maintaining ecosystem functions and providing vital services. This study assessed the nematode diversity and food web structure in flooded rice fields in the main rice producing regions in Portugal. Soil samples were collected from rice fields along the basin of rivers Tagus, Mondego, and Sado in Portugal. Nematodes were extracted and identified to genus level to perform community analyses. Plant-parasitic nematodes (PPN) were identified to species level using 28S rDNA, 18S rDNA and COI markers. The study found 18 nematode genera associated to rice, including bacterivores, fungivores, omnivores, predators and PPN. Based on prominence value, the genus Rhabditis was found to be the most frequent followed by Panagrolaimus and Helicotylenchus. Nematode community composition differed significantly among regions, with small temporal shifts. Diversity patterns were also region specific; the Mondego basin showed the highest diversity index, while richness and evenness across basins remain stable. Functional diagnostics indicated enrichment-dominated food webs across regions, with Tagus and Mondego showing higher food-web structure than Sado. Molecular analysis identified eight PPN species, among which H. dihystera and Pratylenchus crenatus were widespread across the three regions, while Aphelenchoides parietinus, Meloidogyne incognita and Paratrichodorus minor were confined to Mondego, Merlinius joctus to Tagus and Xiphinema citricolum to Sado. Meloidogyne graminicola, the most serious pest of rice worldwide, was not found in Portuguese rice fields. These results provide the first baseline for nematode diversity and food-web condition in Portuguese rice agroecosystems and represent one of the first ecological characterisations of nematode communities in Europe, offering vital information for monitoring and management programmes.