Morphological deformities in parts of the head capsule of Chironomus spp. larvae inhabiting three polluted rivers (Permatang Rawa [PRR], Pasir [PR], and Kilang Ubi [KUR]) in the Juru River Basin, northeastern peninsular Malaysia, were studied. Samples of the fourth-instar larvae at one location in each river were collected monthly from November 2007 to March 2008 and examined for deformities of the mentum, antenna, mandible, and epipharyngis. At each sample location, in situ measurements of water depth, river width, water pH, dissolved oxygen, and water temperature were made. Samples of river water and benthic sediments were also collected monthly from each larval sample location in each river and taken to the laboratory for appropriate analysis. Total suspended solids (TSSs), ammonium-N, nitrate-N, phosphate-P, chloride, sulfate, and aluminum content in water were analyzed. Total organic matter and nonresidual metals in the sediment samples were also analyzed. Among the three rivers, the highest mean deformity (47.17%) was recorded in larvae collected from KUR that received industrial discharges from surrounding garment and rubber factories, followed by PRR (33.71%) receiving primarily residues of fertilizers and pesticides from adjacent rice fields, and PR (30.34%) contaminated primarily by anthropogenic wastes from the surrounding residential areas. Among the various head capsule structures, deformity of the mentum was strongly reflective of environmental stress and amounted to 27.9, 20.87, and 30.19% in the PRR, PR, and KUR, respectively. Calculated Lenat's toxic score index satisfactorily explained the influence of prevailing environmental variables on the severity of mentum deformities. Redundancy analysis and forward selection selected TSSs, sediment Zn, Mn, Cu, and Ni, and water pH, dissolved oxygen, water temperature, total organic matter, nitrate-N, chloride, phosphate-P, ammonium-N, sulfate, and aluminum as parameters that significantly affected some proportion of deformities. The total deformities correlated closely with deformities of mentum but only weakly with deformities in other parts of head. The total deformity incidence was strongly correlated with high contents of sediment Mn and Ni. The mentum and epipharyngis deformities incidence was highly correlated with an increase of TSSs, total aluminum, and ammonium-N and a decrease in pH and dissolved oxygen.