Surface water quality was examined to determine spatial and seasonal variations in the Lower Kinabatangan River catchment, Sabah, Malaysia between October 2004 and June 2005, during the weak La Niña event. The study sought to distinguish between the quality in surface waters draining from an oil palm plantation (OP), a secondary forest (SF) and an oxbow lake (OB); and to identify its seasonal variability. A total of 45 samples were collected during fieldwork campaigns that spanned over the inter-monsoonal period, wet and dry seasons. The Water Quality Index (WQI) was calculated and analysed based on the Malaysia Interim National Water Quality Standard (INWQS). Results show that the quality of the river fall into Class II or moderate level. Discriminant analysis (DA) has been employed to classify independent variables into mutually-exclusive groups. Suspended sediment (SS) and chemical oxygen demand (COD) parameters were found higher during the wet season. COD was found dominant in stream located within the oil palm plantation, whilst SS was dominant in oxbow lake. Surface water quality variations could be influenced by weak La Niña event in 2005/2006, as precipitation anomalies have been observed during the sampling campaign.