Maintenance of suitable conditions in lowland rivers for both fish passage and resident species is crucial to ensuring the long-term sustainability of fish populations. The dissolved oxygen concentration of water is a key factor controlling habitat quality for fish and a critical measure of stream health. Continued land use intensification and greater exploitation of water resources has contributed towards increasing the frequency and duration of low dissolved oxygen events in lowland rivers and the associated risk of adverse effects on fish communities. Revised guidelines are therefore proposed to support setting of biologically relevant dissolved oxygen limits for the protection of New Zealand freshwater fish communities. These guidelines account for both event magnitude and duration, identify different protection levels based on the risk of negative impacts and are based on current scientific knowledge on the tolerances of New Zealand fish species.