The levels of fluctuating asymmetry [random differences between symmetric organismal traits, fluctuating asymmetry (FA)] in the fourth instar of Chironomus spp. larvae inhabiting an agrochemical polluted river [Permatang Rawa River (PRR)] in the Juru River Basin, northeastern peninsular Malaysia, were measured. The PRR receives waters primarily from adjacent rice fields which are exposed to fertilizer and pesticide residues. Samples of larvae, water, and sediments were collected monthly from November 2007 to June 2008. In situ measurements of water pH and dissolved oxygen were made at three sampling locations along the river. Monthly water and benthic sediment collections were also conducted for the following laboratory water analyses: biological oxygen demand (BOD), chemical oxygen demand (COD), total suspended solids (TSS), and ammonium-N content. Non-residual metals in the sediment samples were also analyzed. The water quality index (WQI) of the PRR was also calculated. This study attempted to relate FA levels based on selected traits of Chironomus spp. larval head capsule (mentum width and first and second antennal segment length) to water quality and sediment heavy metal contamination in the PRR. All monthly measurements of FA levels including transcriptors (FA10a, FA4a, ME3, and ME1) and indices [FA, absolute asymmetry (AbsFA), and composite fluctuating asymmetry (CFA)] were calculated. The ordination model of redundancy analysis showed that the dissolved oxygen and water quality in the river expressed as WQI were negatively correlated with all FA indices (FA, AbsFA, and CFA) of the larval mentum width and length of antennal segments I and II. The water pH, BOD, and COD and sediment Cu positively influenced the FA incidence in the larval mentum. The FA indices of the antennal segment I were positively correlated with the increase in the levels of water pH, ammonium-N, BOD, and COD. The FA indices, especially CFA, were sensitive to the water pH and ammonium-N and sediment contaminated by Mn, Cu, and Zn. The FA levels calculated as FA indices of the larval antennal segment II length were positively correlated with water TSS and sediment Mn, Cu, Zn, Water Air Soil Pollut (2011) 216:203-216