Perak River, the second longest river in Peninsular Malaysia supplies water mainly for domestic, agricultural and industrial purposes, whilst contributing to the state�s economy along the river. However, the increasing demand for water has strained anthropogenic environmental pressures on the river basin itself. This paper presents the findings of a toxicological study conducted to evaluate pollution levels in the Perak River using Allium cepa (AC) assay, an excellent biological indicator of pollution that is frequently used in environmental monitoring studies. The water samples, both treated and raw, were taken from 3 water treatment plants (WTPs), namely Parit (P), Kampung Senin (KS) and Teluk Kepayang (TK). ACs were grown in these water samples for a 96-hour period of exposure at 22°C of incubation temperature. The presence of cytotoxic and genotoxic substances in the water samples collected from Perak River were confirmed based on root morphology deformation and cytogenetic alterations observed in the root meristem cells of the ACs. © 2016 Taylor & Francis Group, London.