Abstract: The effect of toxic chemicals on aquatic lives has been a problem in many communities and populations around the world today. Ekerekana and Okochiri communities in Okrika local government area of Rivers state Nigeria, whose river channel is a receptacle to Nigeria National Petroleum Corporation Port Harcourt Refinery’s effluent is not an exemption. It is perceived that this effluent has a negative ecological and human health impact on the affected communities. This study involved the use of Histology as a biomarker to tackle these environmental problems. The ecotoxicological study was carried out in Ekerekana (EKE station) and Okochiri (OKO station), while an aqua-culture centre – African Regional Aquaculture Centre (ARAC) at Buguma, Rivers state was used as the reference or control site. This followed a gross anatomical study of harvested fishes by applying a condition Factor (CF) equation and a fish health assessment index (HAI) protocol. Histological assessment protocol in a qualitative and semi-qualitative scenario was also done. The Environmental Water Quality Index (EWQI) result for the experimental sites were poor (10.5) and marginal (57.5) for EKE and OKO respectively. Sediment quality show elevated Pd. A comparative fish study shows: no significant difference for CF in ARAC (4.62) and OKO (6.65); HAI was better in ARAC (16.0) than OKO (55.5). This study was ecologically relevant; it revealed that Ekerekena and Okochiri creeks are contaminated with a moderate level of pollution.