Estuarine environments are particularly vulnerable to human impacts. In this study, trace elements in Ruppia megacarpa, Halophila ovalis, sediment and porewater were analysed to assess the potential contamination of the Leschenault Estuary, Western Australia, from a primarily agricultural drain. Sediment concentrations of Cd, Cu, Mn, and Ni and were highest nearest the drain while Al, As, Cr, Fe and Zn and were highest further from the drain. H. ovalis showed greater accumulation of Fe, Al, and As than R. megacarpa. Concentrations of Fe, Al, As, and Ni were generally higher in below-ground plant parts than above, suggesting uptake of these trace elements via the sediment-route pathway. This study suggested that the drain was a source of Cu and Mn, with these elements entering the estuary through water inflows. As and Fe, were highest furthest from the drain suggesting input of trace elements from sources other than the drain under study.