This study was aimed at determining the concentration of pyrethroid in the surface water, sediment, Weyonia acuminata and Synodontis clarias fish in Lekki lagoon, Lagos, Nigeria. In-situ physicochemical analysis of the surface water was conducted using a calibrated handheld multi-parameter probe (Horiba Checker Model U-10). Intestinal samples from infected and uninfected fish were analyzed for pyrethroid concentrations, microbial colonization, proteins (PRO), superoxide dismutase (SOD), catalase (CAT), reduced glutathione (GSH), malonaldehyde (MDA) and glutathione peroxidase (GPx). The histopathology of infected and uninfected intestinal tissues were analyzed using Haematoxylin and Eosin (H&E) stains and examined under a binocular light microscope (Model 230485). A total of 39 out of 98 S. clarias fish were infected with cestode parasite, Wenyonia acuminate, amounting to 39% parasite prevalence. Among the tested pyrethroids, Cyfluthrin and Alpha -cypermethrin had significant sorption of 1.62 and 3.27 respectively from the aqueous phase to the bottom sediment of the lagoon. Pyrethroid concentration was in the order of sediment > parasite> water > intestine> liver. The cholesterol, triglycerides, and LDL (low density lipids) in the parasite were higher than in the host fish (p<0.05). On the other hand, the fish hepatic protein, high density lipids (HDL) and glucose were higher than the levels in the parasites (p<0.05). There was a high prevalence of gut microbes (30 - 40%), which include Salmonella sp, Escherichia coli, Pseudomonas sp and Bacillus sp among individuals infected with gut Cestodes, Wenyonia sp compared with uninfected individual which had higher gut Staphylococcus sp., Klebsiella sp., and Proteus sp. (10- 40%). among the congeners of pyrethroids analyzed, Cyfluthrin > Alpha-Cyermethrin had significant sorption on the sediment, however unlike a benthopelagic fish, no pyrethroid was accumulated in the S. clarias from the sediment. The fish however accumulated Alpha-Cypermethrin from the aqueous phase. The parasite on the other hand accumulated Bathroid significantly from the surface water and bottom sediment which may be linked to the higher stress levels observed in the parasite than the host fish. The parasite in turn inflicted histological alterations on the host intestine, marked by moderate inflammation of mucosa, alteration of the villi microstructure, moderate stunting of the villous structure and moderate fibrosis of villous structure. The study demonstrated the efficiency of histopathological and microbial analysis in biomonitoring studies enteric parasites and early detection of pyrethroid toxicity respectively compared to bioaccumulation analysis.