A comprehensive study of the chemical composition of rainwater was carried out from October 2016 to September 2017 in the equatorial tropical rainforest region of northwestern Borneo. Monthly cumulative rainwater samples were collected from different locations in the Limbang River Basin (LRB) and were later categorized into seasonal samples representing northeast monsoon (NEM), southwest monsoon (SWM), and inter-monsoon (IM) periods. Physical parameters (pH, EC, TDS, DO, and turbidity), major ions (HCO3-, Cl-, Ca2+, Mg2+, Na+, and K+) and trace metals (Co, Ni, Cd, Fe, Mn, Pb, Zn, and Cu) were analyzed from collected rainwater samples. Rainwater is slightly alkaline with mean pH higher than 5.8. Chloride and bicarbonate are the most abundant ions, and the concentration of major ions in seasonal rainwater has shown slight variation which follows a descending order of HCO3-> Cl-> Na+ > Ca2+ > Mg2+ > K+ in NEM and Cl- > HCO3- > Na+ > Ca2+ > K+ > Mg2+ in SWM and Cl- > HCO3- > Na+ > Ca2+ > Mg2+ > K+ in IM period. Trace metals such as Fe and Ni have shown dominance in seasonal rainwater samples, and all the metals have shown variation in concentration in different seasons. Variation in chemical characteristic of seasonal rainwater samples identified through piper diagram indicates dominance of Ca2+-Mg2+-HCO3- and mixed Ca2+-Mg2+-Cl- facies during NEM, SWM, and IM periods. Statistical analysis of the results through two-way ANOVA and Pearson's correlation also indicates significant variation in physico-chemical characteristics. This suggests a variation in contributing sources during the monsoon seasons. Factor analysis confirmed the source variation by explaining the total variance of 79.80%, 90.72%, and 90.52% with three factor components in NEM, SWM, and IM rainwater samples with different loading of parameters. Enrichment factor analysis revealed a combined contribution of marine and crustal sources except K+ which was solely from crustal sources. Sample analysis of backward air mass trajectory supports all these findings by explaining seasonal variation in the source of pollutants reaching the study area. Overall, the results show that the chemical composition of seasonal rainwater samples in LRB was significantly influenced by natural as well as anthropogenic processes. These include (long-range and local) industrial activities, fossil fuel combustion, forest burning, transportation activities including road transport and shipping activities, and land-derived soil dust along with chemical constituents carried by seasonal wind.