An ecological threat was recorded in El-Wadi Drain and its discharging area into the upper part of Wadi El-Rayian Lakes during June 11^th, 2001, conducting in mass death of fishes. Water samples were collected from different locations. Structure and density of phytoplankton, zooplankton and bacteria were investigated as the main biological indices which could explain some criteria about the status of the environmental conditions which caused the problem. A total of 62 phytoplankton and 24 zooplankton taxa were identified and counted in the investigated samples. In the drainage water; density of both phyto and zooplankton were low comparing to that recorded under the common environmental conditions. Also, most of the recorded taxa in the drain were specific to polluted environment and completely different with that inhabiting the lake. Diatoms were dominated phytoplankton and most recorded genera (Aulacoseira, Navicula, Nitzschia and Euglina) are being tolerant to high organic pollution. Zooplankton was represented by only two species of Rotifers (Lucane hulla and Cephalodella sp) in addition to limited number of Protozoa (Ciliophora sp.) and free living nematodes. Bacteriological status indicated that saprophytic and parasitic (total bacterial counts) ratio was lower than 1 and its population was maximized to 65x10¹¹/cm³. It was predicted that the drainage water might subjected to heavy polluted conditions. This conclusion was confirmed by high density of most probable number for both total and faecal coliforms (460 and 95x10⁶/cm³) which is characterized to the raw sewage pollution. Finally it was concluded that high amount of raw sewage was drained off in El-Wadi Drain water. Such pollution created sudden disturbance in the existence aquatic environment and exerted a destructive interaction with in the aquatic organisms and could result in the sudden death of fishes.