Despite well documented studies on metal pollutants in aquatic ecosystems, knowledge on the combined effects of catchment characteristics, sediment properties, and emerging pollutants, such as microplastics (MPs) on the presence of metals in urban river sediments is still limited. In this study, the synergistic influence of MPs type and hazard indices, catchment characteristics and sediment properties on the variability of metals present in sediments was investigated based on a typical urban river, Brisbane River, Australia. It was noted that the mean concentrations of metals in Brisbane River decreases in the order of Al (94,142 ± 12,194 μg/g) > Fe (62,970 ± 8104 μg/g) > Mn (746 ± 258 μg/g) > Zn (196 ± 29 μg/g) > Cu (50 ± 19 μg/g) > Pb (47 ± 25 μg/g) > Ni (25 ± 3 μg/g) while the variability of metals decreases in the order of Pb > Cu > Mn > Al > Ni > Zn > Fe along the river. According to enrichment factor (Ef) contamination categories, Mn, Cu and Zn exert a moderate level of contamination (Ef > 2), while Fe, Ni, and Zn show slight sediment pollution (1 <Ef < 2). In the case of Pb, extremely high enrichment (Ef > 3) was found at sampling locations having a high urbanisation level and traffic related activities. Crustal metal elements (namely, Al, Fe, Mn) were found to be statistically significantly correlated with sediment properties (P < 0.05). Anthropogenic source metals (namely, Cu, Ni, Pb, Zn) were observed to be highly correlated with catchment characteristics. Additionally, the presence of metals in sediments were positively correlated with MPs concentration, and negatively correlated with MPs hazard indices. The outcomes of this study provide new insights for understanding the relationships among metals and various influential factors in the context of urban river sediment pollution, which will benefit the formulation of risk assessment and regulatory measures for protecting urban waterways.