Extensive networks of deep drains are being built in Western Australia to reduce the effects of dryland salinity on agricultural lands. Most of these drains discharge into natural river and wetland systems, with little consideration given to the environmental impacts. This study examined the downstream ecological impacts of one of the oldest deep drain networks in Western Australia, located in the Wakeman subcatchment near Narembeen. Twelve sites were sampled bi-monthly from October 2004 to September 2006. On each occasion, water quality parameters were measured and the macro-invertebrate fauna was sampled. Significant differences in water quality and macro-invertebrates were observed between the untreated sites and those affected by the drain discharge. Surface water at untreated sites was always fresh (\3 ppt), alkaline (pH 7.6–8.9) and turbid (49–600 NTU), whereas treatment sites were always saline (28–147 ppt), acidic (pH 1.9–3.8) and mostly clear (0–100 NTU). No recovery of water quality was observed with distance from discharge point (20 km). Invertebrates reflected differences in water quality, with drain discharge resulting in a sharp decline in species richness, and significant changes in macro-invertebrate community composition. Sites affected by drain discharge were dominated by fly larvae such as Orthocladiinae and Ceratopogonidae. Microcrustaceans were far more abundant at sites unaffected by drainage. The ecological values of Wheatbelt streams are likely to be further compromised by discharge of poor water quality from deep drainage.