Flash flooding in the Borough of Queenscliffe occurs as a result of short duration, high intensity rainfall which can cause localised flooding within the municipality along overland flow paths when the urban drainage system surcharges. Flooding from these storms occurs with little warning and localised damage could occur.

The Borough of Queenscliffe also experiences storm surge events, where weather conditions like storms and low-pressure systems increase sea water levels. This can cause damage to coastal infrastructure and can lead to flooding of low-lying coastal land when combined with gale-force onshore winds.

Storm surge events are expected to occur more often and more intensely in future due to climate change.