Macroinvertebrates can be highly sensitive to elevated salinity in freshwater environments, but little is known of the effects of anthropogenic saline discharges on the assemblages, including flow-dependent and still-water forms, in tropical seasonally-flowing streams. Magnesium (Mg) is a mine‐related contaminant and is a potential environmental risk to receiving waters in Kakadu National Park, tropical northern Australia. The macroinvertebrate assemblage in a seasonally-flowing stream in the wet-dry tropics was characterised at four stages of the hydrograph, from early wet season flow to early dry season pools at flow cessation. On each of the four occasions, a range of the most abundant macroinvertebrate species were collected and acutely exposed to a range (up to 19) of Mg concentrations under laboratory conditions. Taxa were ranked in order of their sensitivity to Mg, which ranged between 39 mg/L Mg (Caenidae: Tasmanocoenis spp.) and 4,400 mg/L Mg (Dytiscidae: Clypeodytes feryi), based on the 50% Lethal Concentration (LC50). Characterisation of the macroinvertebrate assemblage at each stage of the hydrograph indicated when Mg-sensitive species are present in the creek channel. The taxa that were most sensitive to Mg were abundant across all stages of the hydrograph indicating that there is no specific period where the risk of Mg impacts to stream macroinvertebrates would be greater.