Irrigation is a dry season agricultural activity that was known to man for centuries. Agricultural runoff has been identified as the major nonpoint sources of pollution into surface waterbodies which changes the physicochemical parameters thereby impacting on the biodiversity of such ecosystem. River Ngadda receives pollutants from the irrigational sites along the river bank. The study was aimed at assessing the impact of irrigation on fish biodiversity in river Ngadda, Maiduguri, Borno State, Nigeria. The objectives of the study were to determine the physico-chemical parameters and examine the fish biodiversity of the river. The river was divided into 4 sampling Stations. Water samples was collected biweekly for the period of 6 months from 4 sampling stations. The physico-chemical qualities (total nitrogen (TN), ammonium (NH4 +), total phosphorus (TP), total organic carbon (TOC), total dissolved solids (TDS), turbidity (Tur) and total suspended solids (TSS) were determined using standard methods. Capture and recapture method was employed to determine the relative abundance of fish species using Lincoln index. The mean Total Nitrogen (TN) ranges from 5.02 mg/L-8.31mg/L, mean ammonium (NH4 +) ranges from 0.93mg/L-2.01, mean Total phosphorous (TP) ranges from 0.07mg/L-1.81mg/L. mean Total Organic Carbon (TOC) ranges 5.87mg/L-7.45mg/L, mean Turbidity (Tur) ranges from 27mg/L-31mg/L, mean Total Dissolved Solids (TDS) ranges 198NTU-298NTU, mean Total Suspended Solids ranges from 34mg/L-47mg/L and mean surface water Temperature ranges from 26°C-28°C. A total of 4 families and 10 species of fishes were identified in the sampling stations.