Anthropogenic activities are contributing to the changing hydrology of rivers, often resulting in their degradation. Understanding the drivers and nature of these changes is critical for the design and implementation of effective mitigation strategies for these systems. However, this can be hindered by gaps in historical measured flow data. This study therefore aims to use sediment cores to identify historical hydrological changes within a river catchment. Sediment cores from two floodplain lakes (billabongs) in the urbanised Yarra River catchment (Melbourne, South-East Australia) were collected and high resolution images, trends in magnetic susceptibility and trends in elemental composition through the sedimentary records were obtained. These were used to infer historical changes in river hydrology to determine both average trends in hydrology (i.e., coarse temporal resolution) as well as discrete flood layers in the sediment cores (i.e., fine temporal resolution). Through the 20th century, both billabongs became increasingly disconnected from the river, as demonstrated by the decreasing trends in magnetic susceptibility, particle size and inorganic matter in the cores. Additionally the number of discrete flood layers decreased up the cores. These reconstructed trends correlate with measured flow records of the river through the 20th century, which validates the methodology that has been used in this study. Not only does this study provide evidence on how natural catchments can be affected by land-use intensification and urbanisation, but it also introduces a general analytical framework that could be applied to other river systems to assist in the design of hydrological management strategies.