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The objective of this study is to understand the association between the Bell River and alluvial and karst aquifers at Wellington, Australia. Two-dimensional resistivity imaging mapped the transition between the alluvium and karst. The water levels in caves, bores within the karst and the alluvium, and in the river were continuously measured. Water samples along the river, and from alluvial and karst monitoring bores and from the caves were collected. Water isotopic composition, chloride and DOC concentrations were determined, absorbance values were measured and fluorescence properties were characterised. The absorbance data were processed to provide the specific ultraviolet absorbance (SUVA) and spectral slopes. Parallel factor analysis (PARAFAC) was applied to discriminate fluorescent DOM components and to assess their dynamics in river and groundwater. The resistivity images delimited a dipping boundary between the low resistivity alluvium and the more resistive limestone, and delimit the water level in the aquifer. There are likely cavities that can act as potential pathways for groundwater flow, connecting Wellington karst aquifer with the alluvial aquifer and the river. Groundwater levels are dynamic and respond quickly to changes in the river stage, implying a strong hydraulic connection, and that the river is losing. The water stable isotope (δ18O and δ2H) and chloride data demonstrate a direct hydraulic connection between the river and groundwater. PARAFAC modelling revealed different models were necessary for river and groundwater samples, with component one of the groundwater model in the ‘peak T’ region, and of the river model in the ‘peak C’ region. Absorbance and fluorescence data suggest that sedimentary organic matter in the alluvium and karst is a major source of groundwater DOM, which is subsequently utilized by microbial activity. Additionally, there is a transition zone in the aquifer adjacent to the river (< 50 m) where DOM concentration, absorbance and fluorescence intensity rapidly decrease from the river to the aquifer, suggesting the groundwater near the river acts as a sink for the riverine organic matter during periods where the river is infiltrating the aquifer.