Understanding challenges posed by climate change to estuaries and their faunas remains a high priority for managing these systems and their communities. Freshwater discharge into a range of estuary types in south‐western Australia between 1990 and 2015 is shown to be related to rainfall. This largely accounts for decreases in discharge in this microtidal region being more pronounced on the west coast than south coast, where rainfall decline was less. Results of an oxygen‐balance model imply that, as demonstrated by empirical data for the Swan River Estuary, declines in discharge into a range of estuary types would be accompanied by increases in the extent of hypoxia. In 2013–15, growth and body condition of the teleost Acanthopagrus butcheri varied markedly among three permanently open, one intermittently‐open, one seasonally‐closed and one normally‐closed estuary, with average time taken by females to reach the minimum legal length (MLL) of 250 mm ranging from 3.6 to 17.7 years. It is proposed that, in a given restricted period, these inter‐estuary variations in biological characteristics are related more to differences in factors, such as food resources and density, than to temperature and salinity. The biological characteristics of A. butcheri in the four estuaries, for which there are historical data, changed markedly between 1993–96 and 2013–15. Growth of both sexes, and also body condition in all but the normally‐closed estuary, declined, with females taking between 1.7 and 2.9 times longer to attain the MLL. Irrespective of period, body condition, and growth are positively related. Age at maturity typically increased between periods, but length at maturity declined only in the estuary in which growth was greatest. The plasticity of the biological characteristics of A. butcheri, allied with confinement to its natal estuary and ability to tolerate a wide range of environmental conditions, makes this sparid and comparable species excellent subjects for assessing estuarine “health.”