Rivers are important drivers in altering the hydrography and consequently the biogeochemistry of oceans whereby the coastal ocean biogeochemistry is affected by fluvial systems which input nutrients.  It is estimated that the concentrations of N and P in the majority of rivers worldwide have at least doubled due to anthropogenic inputs. However, understanding the dynamics of the Rajang river in which it largely passes through peat-domes and has mass discharge of organic matter caused by both natural and anthropogenic activities may be a challenge.   Hence, in this study, the main aim is to determine the spatial and temporal variations in nutrient budgets of the Rajang river-sea continuum and its influence on the phytoplankton functional groups will be determined along with the main drivers for such variations.  Three sampling campaigns (August 2016, March 2017 and September 2017) were undertaken along ~300km of the Rajang river to study both spatial and temporal/seasonal distribution of nutrients as well as phytoplankton pigments (community) distribution. The analyses for nutrients encompass both inorganic (i.e Nitrate, NO3-, Nitrite, NO2-, Ammonium, NH4+, Phosphate, PO4- and Silicate. SiO4-) as well as organic (Dissolved organic nitrate and Dissolved organic phosphate) fractions which were carried out utilizing a SKALAR San++ continuous flow analyser. Moreover, the nutrients analyses obtained will be utilized for nutrient budget models (LOICZ) in order to interpolate the regional nutrients budget. Lastly, the phytoplankton pigments will be processed and analysed via GC-MS and the data will be processed utilizing the CHEMTAX software for seasonal and temporal phytoplankton community structure profiling and coupling with nutrient budgets. Early results of Spearman’s Rank from the first cruise (August 2016) show that PO4- is moderately correlated  to salinity (0.57) while NO3- and SiO44- are strongly negatively correlated to salinity (-0.90 and -0.97 respectively).  Furthermore,  NO3-  is strongly correlated to SiO44- (0.86), indicating possible origin of NO3- and SiO44- from the perturbation of headwaters as compared to the river mouth (coastal region). Also, the Redfield’s ratio from the averaged values of Dissolved inorganic nitrogen (DIN): Dissolved Inorganic Phosphate (DIP) indicates phosphate limitation within the rivers, which has implications for the phytoplankton community as well as primary productivity. While the initial results obtained are yet unable to project a complete understanding of the nutrient budgets and its dynamics within the phytoplankton community, it is an important baseline to further elucidate the contribution of materials from the Rajang River into the South China Sea.