This research dealt with the ectoparasitic helminth communities infesting the African sharptooth catfish, Clarias gariepinus Burchell, 1822 and the Nile tilapia Oreochromis niloticus Linnaeus, 1758 inhabiting the degraded aquatic environments of the Nile Delta, Egypt, from summer 2021 to spring 2022. The study was carried out in four interconnected locations: Nezam Drain, a typical agricultural drainage system; Amlak Drain, which is heavily polluted from multiple sources; and two smaller agricultural drains (MAS-1 and MAS-2) linked to Amlak and Nezam Drains, respectively. Amlak Drain notably releases water into Manzala Lake, a crucial habitat for local fish populations. The investigation involved 246 specimens of C. gariepinus, which yielded 6,361 monogenean worms across six species. In comparison, 124 specimens of O. niloticus produced 450 pathogenic microorganisms, comprising six monogenean and one digenean species. Using Jaccardʼs index, the study found complete similarity (Sj=100%) in monogenean communities of C. gariepinus across all habitats and a high similarity (Sj=87.5%) for O. niloticus between MAS-1 and MAS-2. The research evaluated both intraspecific and interspecific aggregation indices, uncovering non-random distribution patterns among monogenean species and indicating a stronger interspecific aggregation that suggests coexistence dynamics. The condition factor (K), which indicates fish health, showed that higher parasite loads adversely affected fish welfare; those with better condition factors (Class III) had lower parasite intensities than those in poorer health classes (I and II). These results emphasize the negative impact of ectoparasitic infections on fish health and highlight how environmental degradation influences the structure of parasite communities. The findings advocate for effective management strategies to address these issues in the Nile Deltaʼs aquatic ecosystems.