The socio-economic impacts of the free-floating aquatic plant water hyacinth, Eichhornia crassipes (Pontederiaceae), on aquatic systems are well documented, yet the impacts on aquatic biodiversity, particularly invertebrate biodiversity, are less well understood. This study aimed to determine whether the presence of water hyacinth altered the diversity and assemblage structure of benthic macroinvertebrates in a conservation area. The benthic macroinvertebrate assemblage was sampled over 1 year at five sites under water hyacinth mats and at five sites without water hyacinth at Lake Nsezi—Nseleni River in the vicinity of Richards Bay, KwaZulu-Natal, South Africa. Artificial substrates were placed beneath water hyacinth mats or in the open water to allow for colonization by freshwater macroinvertebrates, and left for a period of 6 weeks, repeated on seven occasions. Twenty nine families comprising 18,797 individuals were collected, 817 (13 families) individuals were from under water hyacinth mat sites compared to 17,980 (27 families) individuals from open water sites. Ninety-eight percent of individuals collected were, however, the invasive snail, Tarebia granifera. Open water samples were separated from samples beneath the water hyacinth mat by non-metric Multidimensional Scaling, indicating reduced biodiversity associated with the presence of water hyacinth. Exclusion of the dominant Thiaridae from the analysis did not alter the groupings. Family richness(s) and abundance (N) were significantly higher in open water communities(S: H3 = 21.09; P = 0.0001; N: H3 = 22.58; P = 0.00001), while evenness (J’) was higher under water hyacinth mats (H3 = 20.13; P = 0.0002). The presence of water hyacinth had a significantly negative impact on aquatic macroinvertebrate biodiversity in a conservation area, and therefore the control of this invasive aquatic plant must play a major role in catchment management.