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The groundwater-dependent ecosystem in the Gnangara region is confronted with great threats due to the decline in groundwater level since the 1970s. The aim of this study is to apply multiple trend analysis methods at 351 monitoring bores to detect the trends in groundwater level using spatial, temporal and Hydrograph Analysis: Rainfall and Time Trend models, which were applied to evaluate the impacts of rainfall on the groundwater level in the Gnangara region, Western Australia. In the period of 1977–2017, the groundwater level decreased from the Gnangara’s edge to the central-north area, with a maximum trend magnitude of −0.28 m/year. The groundwater level in 1998–2017 exhibited an increasing trend in December–March and a decreasing trend in April–November with the exception of September when compared to 1978–1997. The rainfall + time model based on the cumulative annual residual rainfall technique with a one-month lag during 1990–2017 was determined as the best model. Rainfall had great impacts on the groundwater level in central Gnangara, with the highest impact coefficient being 0.00473, and the impacts reduced gradually from the central area to the boundary region. Other factors such as pine plantation, the topography and landforms, the Tamala Limestone formation, and aquifer groundwater abstraction also had important influences on the groundwater level.

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As significant players in material cycling and energy flow, bacteria and eukaryotes play a vital role in the ecosystem. Nevertheless, the community dynamics of bacteria and eukaryotes in rivers and their responses to changes in ecological hydrology have not been studied thoroughly. Based on eDNA technology, this study investigated the bacterial and eukaryotic communities in the upper, middle and lower reaches of the Weihe River in different seasons. The seasonal variation and geographical distribution of bacterial and eukaryotic community structures showed significant heterogeneity. The selective theory well explained the response of microbial community assembly to seasonal changes. Deterministic processes dominate microbial community assembly in the middle and lower reaches. The composition and metabolic potential of key functional genes of nitrogen and phosphorus cycling (nosZ, pqqB, pqqD, and pqqE) exhibited strong seasonal patterns and were significantly correlated with the physical and chemical properties of water. There were significant differences in molecular ecological networks in different periods (p < 0.05), with a gradually increasing trend in the complexity of the network from winter to summer. The keystone species (Hub) of the microbial food web in each season included microorganisms (Malikia), algae (Stephanodiscus), and invertebrates (Polyarthra). Structural equation modeling (SEM) results indicated that invertebrate was an important driving factor affecting the changes in community structures. In micro-food webs, both “bottom-up” (resources) and “top-down” (predation) forces strictly controlled the relationship between taxa. Nitrogen and phosphorus concentrations affected microbial networks, and there was a significant correlation between bacterial and eukaryotic groups and eco-hydrological variables (p < 0.05). Furthermore, we identified the taxon’s change point using threshold indicator taxa analysis (TITAN), quantitatively revealing the response thresholds of taxa to eco-hydrological changes.