Potentially toxic elements (PTEs) contamination in Wainivesi River, Fiji triggered by gold-mining activities is a major public health concern deserving attention. However, chemometric approaches and pattern recognition of PTEs in surface water and sediment are yet hardly studied in Pacific Island countries like Fijin urban River. In our study, twenty-four sediment and eight water sampling sites from the Wainivesi River, Fiji were explored to evaluate the spatial pattern, eco-environmental pollution, and source apportionment of PTEs. This analysis was done using an integrated approach of self-organizing map (SOM), principle component analysis (PCA), hierarchical cluster analysis (HCA), and indexical approaches. The PTEs average concentration is decreasing order of Fe > Pb > Zn > Ni > Cr > Cu > Mn > Co > Cd for water and Fe > Zn > Pb > Mn > Cr > Ni > Cu > Co > Cd for sediment, respectively. Outcomes of eco-environmental indices including contamination and enrichment factors, and geo-accumulation index differed spatially indicated that majority of the sediment sites were highly polluted by Zn, Cd, and Ni. Cd and Ni contents can cause both ecological and human health risks. According to PCA, two sources such as point and geogenic sources for sediment and also two sources including weathering of rock-water and anthropogenic sources of PTEs for water were identified in the study area. The SOM analysis identified three spatial patterns e.g., Cr-Co-Zn-Mn, Fe-Cd and Ni-Pb-Cu in water and Zn-Cd-Cu-Mn, Cr-Ni and Fe, Co-Pb in sediment. Spatial distribution of entropy water quality index values depicted that northern and northwestern areas possess ‘poor’ to ‘extremely-poor’ quality water. The entropy weights indicated Zn, Cd and Cu as the major pollutants in deteriorating the water quality. Our finding provides a baseline database with eco-environmental and health risk measures for the Wainivesi river contamination.