This study was to determine the heavy metal pollution study of fresh water Ecosystem in parts of Sombriore and Orashi River catchement area at Agba-Ndele and Ikiri River, Rivers State. Field sampling was conducted across several locations along the Rivers, with laboratory analysis carried out to measure water quality parameters, sediment characteristics, and heavy metal concentrations. Twenty-five species of benthic macro-invertebrates belonging to Seven (7) classes were identified in Agba- Ndele River, while twenty-nine (29) species were also recorded in Ikiri River, with the class insect having the highest percentage of 44.0% in Agba-Ndele followed by Gastropoda and Olgochaeta with (6.0%) each, Hirudinea and Crustacea (8.0%) each, and Chetellata and Arachnida (4.0%). Ikiri recorded percentage composition of (48.3%) in Insecta, followed by Oligochaeta and Gastropoda (13.8%) each, Crustacea (10.3%), Hirudinea (6.9%), while Chitellata and Arachnida recorded the same percentage of (3.4%) each. In terms of abundance, Agba-Ndele recorded (60.0%) of Oligochaeta, followed by Insecta (24.9%), Gastropoda (5.9%), Crustacea (4.5%), Hirudinea (2.5%), Chitellata (1.3%) and Arachnida had the least of (0.8%). Bacillariophyceae dominated the planktonic community, making up (83.9%) in Ndele River and (50.9%) in Ikiri River, zooplankton populations were represented by protozoa, copopoda and Nematoda. The diversity index were to assess species richness which recorded 1.029 in Agba-Ndele and 0.032 in Ikiri River. This search contributes significant to the understanding of aquatic biodiversity and the ecological impacts of pollution in the Niger Delta region.