The common hippopotamus (Hippopotamus amphibius) is a keystone megaherbivore endemic to sub-Saharan Africa. Despite this ecological importance, the species is listed as Vulnerable by the International Union for Conservation of Nature due to habitat loss and increasing human–wildlife conflict. An under-recognized threat for human, livestock and wildlife health is the impact of parasitic infections, particularly snail-borne trematodiases. However, the role of intermediate hosts in maintaining and dispersing these wildlife parasites remains poorly understood. This gap is especially concerning in biodiversity hotspots, where conservation efforts may be undermined by invasive freshwater snails altering parasite transmission. To address this, trematode diversity in hippopotamuses and associated freshwater snail communities was investigated in the Greater Kruger region using morphological and molecular approaches. Six snail species were recorded, including the invasive exotic Tarebia granifera. The first trematode infection in this species in Southern Africa is reported here, identifying the non-native intestinal fluke Haplorchis taichui and suggesting a potential co-invasion event. In hippopotamuses, infections with Schistosoma edwardiense, S. hippopotami and Fasciola nyanzae were confirmed. Additionally, three amphistome taxa were isolated from hippopotamus carcasses, including Gigantocotyle gigantocotyle, Nilocotyle praesphynctris and the first South African record of Carmyerius aff. schoutedeni. This study provides a molecularly informed parasitological baseline for a subregion of the Greater Kruger system and highlights the role of invasive hosts in reshaping parasite transmission within protected freshwater ecosystems. The detection of a potentially co-invaded trematode underscores the importance of integrating wildlife, invasive species and disease ecology in understanding emerging risks under global environmental change.