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.”

Shellfish reefs have been lost from bays and estuaries globally, including in the Swan-Canning Estuary in Western Australia. As part of a national program to restore the ecosystem services that such reefs once provided and return this habitat from near extinction, the mussel Mytilus galloprovincialis was selected for a large-scale shellfish reef construction project in this estuary. To assess the potential filtration capacity of the reef, estuary seston quality, mussel feeding behavior, and valve gape activity were quantified in the laboratory and field during winter and summer. In general, estuary water contained high total particulate concentrations (7.9–8.7 mg L⁻¹). Standard clearance rates were greater in winter (1.9 L h⁻¹; 17 °C) than in summer (1.3 L h⁻¹; 25 °C), the latter producing extremely low absorption efficiencies (37%). Mussel valves remained open ~97% and ~50% of the time in winter and summer, respectively. They often displayed erratic behavior in summer, possibly due to elevated temperatures and the toxic microalgae Alexandrium spp. Despite numerous stressors, the reef, at capacity, was estimated to filter 35% of the total volume of the estuary over winter, incorporating 42.7 t of organic matter into mussel tissue. The reefs would thus make a substantial contribution to improving estuary water quality.