Hydrological variables of a catchment and their corresponding extreme characteristics have a possibility of switching regimes, particularly when a catchment undergoes protracted dry periods. This can result in a catchment experiencing a flow anomaly that is even more extreme than what was historically considered an extreme low flow event for the catchment. Catchments in southeast Australia have been shown to exhibit multiple states of mean annual flows. Given this and studies that suggest that extreme events may be changing with time, it is important to understand whether extremes in flows also have the potential to exist in multiple states. To investigate this, we studied intensity, duration, and frequency (IDF) of low flows for 161 unregulated catchments in southeast Australia. A Hidden Markov Model-based approach was used to examine shifts in the low flow characteristics. We found very strong evidence of low flow intensity exhibiting two distinct states for at least 34 (21%) catchments in the region, providing convincing reasons to believe that extremes in low flows can and have undergone regime changes. The second state of these catchments is often associated with higher values of low flow intensities. Simulation of the duration and frequency of these events, however, needs improvement with the current approach and may be better studied by accounting for climate indicators that may more suitably explain them. Impacts from a changing climate may enhance the triggering of low flows into alternate states, which calls for water managers to plan for changing regimes of extremes.