Environment Southland has warned people against water-based activities at New River Estuary.
The river mouth is emitting a foul odour and producing black soil.
Coastal scientist Nick Ward says a number of people have complained about the smell and sediment, but the cause is not yet known.
Mr Ward believes it could be due to the huge algae growth in the river mouth over the past few years which has resulted in organic matter smelling like rotten eggs.
The odour could also be a result of low river levels, low tides and warm conditions, he says.