The characteristics dissolved organic matter (DOM) and surface water quality in Maliau Basin, Sabah, Malaysia, were determined from December 2014 to September 2015. The objectives of this study were: (i). to distinguish the surface water quality of rivers which consisted of different types of land use: primary forest (PF), secondary forest (SF), main river (MR) and altered habitat (AH); (ii). to assess seasonal variations of the water quality. A total of 36 water samples were collected during the fieldwork campaign that extended over high and low rainfall periods. The water quality physico-chemical parameters such as water temperature, pH, dissolved oxygen (DO), conductivity, and salinity were measured in-situ with the YSI-multiparameter instrument, while dissolved organic carbon (DOC) concentration was evaluated using Shimadzu TOC-V-SCH analyzer with auto-sampler TOC-ASI-V equipped. Dissolved organic matter (DOM) was determined optically in the laboratory at 254 (a254), 340 (a340) and 410 (a410). Discriminant analysis (DA) was employed to organize independent variables into mutually-exclusive groups. The outcome of DA indicated that water temperature, total suspended solid (TSS), and conductivity were dominant at AH, whilst a340 was dominant at MR in March 2015. Our results also showed seasonal variations for water quality parameters. The highest mean concentrations of pH and a340 were found during the dry period (March 2015) and dissolved oxygen (DO) during the wet season (December 2014), suggesting spatio-seasonal variations of DOM and water quality parameters were determined by environmental factors such as precipitation, water velocity and discharge amount. UV-vis absorptions a254 and a340 show significant positive correlation with dissolved organic carbon (DOC), suggesting that it could be a suitable proxy for DOC concentration for tropical flowing water.