INTRODUCTION Excess nutrients in waterways contribute to eutrophication and poorer aquatic ecosystem health, a problem affecting rural and urban catchments. Key nutrients such as nitrogen and phosphorus can move between the stream bed sediment and water column due the influence of physical, chemical and microbiological factors in the stream environment, which affect their availability and resulting ecological impact. In order to address excess nutrient problems in urban waterways, authorities have been developing strategies to mitigate impacts by using inchannel and land-based stormwater treatment to remove pollutants via settling and other physical, chemical and/or biological processes. However, little is known about how pollutants are transported and transformed in these urban in-channel systems under the influence of different groundwater conditions. Therefore, this research aims to understand the dynamics of nutrients (nitrogen and phosphorus) in waterways systems under the influence of different groundwater conditions (seepage, neutral, and drainage). It was hypothesized that groundwater and bed material characteristics affect the concentration and form of pollutants, as well as their mobility. This understanding could help guide stream management decisions.