Estuaries have many ecological roles, including nutrient cycling and acting as buffer zones by protecting coastal habitats, including human settlements, in case of extreme weather events such as flooding. However, estuaries are vulnerable to increased anthropogenic pressures, such as nutrient enrichment and hydrological modifications, and are already experiencing higher frequencies of severe weather events due to climate change. Here, we investigate how an ecological role of an estuary, i.e. the microbial driven cycling of key nutrients, is impacted by and recovers after a major flood event. We use the Brisbane River Estuary (BRE) as a model system, which has seen historic flooding and has experienced a recent major flood event (March 2022). For our analysis, we utilized multi-omics (metagenomics, meta-transcriptomics and single-cell omics) on samples from a 14 months time-series to analyze the impact of the 2022 flood event on the prokaryotic community, and their nutrient cycling related functions. Our results revealed that the flood introduced considerable changes to the prokaryotic community, e.g. the proliferation of, opportunistic taxa, which likely benefit from flood conditions, as opposed to recovering taxa, which showed low to undetectable relative abundances during the flood but slowly returned to pre flood levels after four months to a year. Inferences of nutrient (carbon, nitrogen, phosphorus, sulfur), and photosynthesis pathways suggested e.g. that ammonia oxidation performed by Nitrosopumilus and Nitrosarcheum was upregulated during the flood, whereas the high transcript expression of the photosynthetic autotrophic Parasynechococcus did not occur until one year post flood. Other taxa, such as the methylotrophic genus BACL14 (order Burkholderiales), were among resilient taxa that were active during the entire time series. Overall, our study showed that estuarine ecosystem functions performed by prokaryotic communities can recover following a major flood event, but that it can take up to one year to restore pre-flood ecosystem services.