The toxicity, persistence, and propensity for accumulation of metals in aquatic environments have raised significant concerns globally. Expansion of urbanization with the growth of industrial and agricultural sectors in Miri City results in a high concentration of pollutants that flow directly into the Miri River. Hence, this study provides a comprehensive analysis of the Miri River water quality, focusing on spatial and temporal variations. River water samples were collected in two different time periods and analysed for physico-chemical parameters includes major ions, nutrients, metals and isotopes. Particularly, the metals were analysed in different size fractions (particulate and colloid) of the suspended solids. Geochemical plots, pollution index, geochemical modelling and factor analysis were used for the data analysis. Interpretation of data reveals that the mean concentration of metals in river water were increased from downstream to the upstream of the river irrespective of the seasons. Major ions were mostly derived from the chemical weathering of source rocks, which was supported by the Gibbs plot. Piper plot indicates the seasonal shifting of water types from Ca–Mg to Na–Cl. Isotopic signatures reveal direct atmospheric precipitation and evaporation were the major origins of river water. Fe was the dominant metal concentration in river water irrespective of the seasons (mean concentration 1.05 mg/L). Fe and Zn were the dominant metal concentration observed in all the 3 size fractions of suspended solids. Industrial activities and seawater influx dominate in the downstream, whereas weathering and agricultural inputs are significant in the upstream of the river. Particulate and colloidal fractions are the major contributors for the metal transport in the midstream and downstream of the river. The outcome of this study offer a thorough understanding of the seasonal elemental distribution at different size fractions, geochemical behaviour and the pollution status of the Miri River. With this knowledge, sustainable management strategies can be developed for this crucial water resource to the benefit of Miri community.