The provision of water to meet the needs of an ever increasing urban population is a significant challenge. This is because urban receiving waters are constantly at risk from pollutant inputs via stormwater runoff and wastewater discharge. This research study employed multiple approaches including principal component analysis, Bayesian Networks (BNs) modelling and geospatial analysis to identify patterns in the distributions of nutrients and metals in water and sediments in an urban river and the interactions between the two phases. In both, water and sediments, nutrient concentrations/loads varied in the order of total carbon (TC) > total nitrogen (TN) > total phosphorus (TP). The river sediments were found to contain the highest crustal metal loads, while in water, the marine-related metals had the highest concentrations. The BNs modelling of pollutant interactions between water and sediment phases indicated that nitrogen is more likely to be transferred from water to sediment than the opposite, while anthropogenic metals are more likely to be transferred from sediments to water. Further, geospatial analysis showed that TN, crustal metals and anthropogenic metal loads in sediments increased from upstream to downstream, while having a decreasing pattern in water. However, marine-related metals in both, water and sediments had increasing concentrations/loads from upstream to downstream. These spatial patterns are attributed to the interactions between water and sediment phases, sediment transport along the river and seawater intrusion in the estuarine area. The study outcomes are expected to contribute to enhancing the knowledge required for developing mitigation strategies to improve urban receiving water quality.