Heteropteran communities form a key component of aquatic ecosystems but have not been widely studied compared to other freshwater faunal groups. This research examined the environmental parameters influencing the diversity, seasonal distribution and structure of aquatic Heteroptera assemblages in the Mediterranean region of Tunisia, northern Africa. Heteropterans were most abundant during spring and summer, coinciding with the emergence of several species and the most favorable environmental conditions for benthic aquatic fauna. Three-way multivariate analyses (combining community composition data from all sites and seasons) highlighted the longitudinal spatial organization of Heteropteran communities. Headwater regions were dominated by halophobic sensitive taxa, and lowland sites were characterized by high salinity resistant taxa (halophilic taxa). The longitudinal organization was driven by gradients of mineralization (salinity and electrical conductivity) and oxygen (DO, COD and BOD) concentrations. Taxonomic composition differed between river catchments, with significantly higher diversity (taxa richness) in the streams with adjacent riparian forest cover. These sites were characterized by the presence of endemic species, such as Velia africana and Velia eckerleini, and rare species, Notonecta meridionalis, and Aquarius najas. Results recorded highlight the importance of aquatic vegetation and water quality in driving the seasonal and spatial variability of Heteropterans, and provide important information to inform the management and conservation of freshwater biodiversity in Northern Africa.