This study has determined how the characteristics of the ichthyofauna of a large eutrophic microtidal estuary changed, initially in response to major structural remedial modifications, and then, during later years, as the environment became further modified, due mainly to effects of climate change. Data on the ichthyofauna of the Peel-Harvey Estuary, in south-western Australia, were derived firstly by seining seasonally in five regions over two consecutive twelve months (two years) in 2008–10. These data were then collated with those recorded previously using the same sampling regime throughout 1980 and 1981, when massive macroalgal growths were present, and throughout 1996 and 1997, soon after the opening, in 1994, of an artificial, deep and second entrance channel. The latter resulted in greater tidal flushing, consistently high salinities and reduced macroalgal biomass. Ichthyofaunal composition changed significantly overall and in four of the five regions across the three periods. Although increased tidal exchange did not lead to a rise in the number either of those marine species that typically use estuaries as nursery areas (marine estuarine-opportunists) or of those that complete their life cycle within the estuary (estuarine residents), the contributions made by the abundances of the representatives of those two groups to the total catch of fish varied markedly between periods. Those differences were largely responsible for the inter-period changes in species composition. In contrast to the situation with marine estuarine-opportunists, increased tidal exchange and higher salinities resulted in a greater number of marine straggler species entering the system, albeit in low numbers. The ichthyofauna during 1980–81 contained relatively large numbers of species that are typically associated with macrophytes, including marine estuarine-opportunists, e.g. Pelates octolineatus, and estuarine residents e.g. Ostorhinchus rueppellii and Hyporhamphus regularis. Following the opening of the artificial entrance channel, the relative abundances of these three macrophyte-associated species declined, whereas those of species, e.g. the marine estuarine-opportunist Torquigener pleurogramma and estuarine resident Favonigobius lateralis, which typically occur over unvegetated areas and in elevated salinities, increased. By 2008–10, such species had become more abundant, following declines in freshwater discharge and a longer persistence of high salinities, with macrophyte-associated species, e.g. the marine estuarine-opportunists P. octolineatus, Gymnapistes marmoratus and Haletta semifasciata and estuarine resident O. rueppellii, becoming more numerous as macroalgal and seagrass areas became better developed. This study demonstrates the great value of long-term data sets for detecting and predicting the effects of major structural changes and climate change on the faunas of estuaries.
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