The Daly River, in the wet-dry tropics of northern Australia, experiences extremes of flow and water clarity. Floods and highly turbid conditions are characteristic of the wet season, supplied by surface runoff from monsoonal rains. Dry season flows are shallow and have low turbidity, and supplied by karst groundwater. Groundwater extraction will affect dry season flows. The high clarity of groundwater-fed flows permits a sequence primary producers, from microscopic to vascular plants, to establish, which provide physical habitat and food source for river fauna. Groundwater management is integral to the river’s dry season ecology.