The apple snail Pomacea spp., a freshwater gastropod native to South America, have become widely established in 11 Asian countries, including Japan. Owing to their feeding on aquatic plants and crops, Pomacea spp. have been considered to be highly invasive, and thereby listed among the “100 of the World’s Worst Invasive Alien Species”. Pomacea spp. are known to be omnivorous, consuming freshwater snails, their eggs and amphibian eggs under laboratory conditions, indicating potential negative impacts on native aquatic communities. However, quantitative assessments of their impacts on freshwater snail communities under natural field conditions remain scarce. To address this gap, this study aimed to evaluate the effects of Pomacea spp. on freshwater snail communities in rice fields. We conducted field surveys at 277 rice paddy sites across Osaka Prefecture, where the species has been widely established, between May 2021 and September 2022. The results showed that the number of native freshwater snail species was significantly lower at sites with Pomacea spp. than at those without. Specifically, when we analyzed the data by reproductive mode—a trait previously suggested to be linked to vulnerability—oviparous species showed a negative association with the presence of Pomacea spp. Furthermore, feeding experiments confirmed that Pomacea spp. directly prey on oviparous snail species. These results suggest that Pomacea spp. negatively affect native freshwater snails, particularly oviparous species.