Payatas landfill in Quezon City, Philippines, releases leachate to the Marikina River through a creek. Multivariate statistical techniques were applied to study temporal and spatial variations in water quality of a segment of the Marikina River. The data set included 12 physico-chemical parameters for five monitoring stations over a year. Cluster analysis grouped the monitoring stations into four clusters and identified January–May as dry season and June–September as wet season. Principal components analysis showed that three latent factors are responsible for the data set explaining 83% of its total variance. The chemical oxygen demand, biochemical oxygen demand, total dissolved solids, Cl− and PO43− are influenced by anthropogenic impact/eutrophication pollution from point sources. Total suspended solids, turbidity and SO42− are influenced by rain and soil erosion. The highest state of pollution is at the Payatas creek outfall from March to May, whereas at downstream stations it is in May. The current study indicates that the river monitoring requires only four stations, nine water quality parameters and testing over three specific months of the year. The findings of this study imply that Payatas landfill requires a proper leachate collection and treatment system to reduce its impact on the Marikina River.