In this study, we integrated metagenome sequencing and metaproteomics to obtain comprehensive taxonomic and functional profiles of microbial communities, investigating the impact of stagnation compared with continuous flow dynamics. To achieve this, we employed laboratory-scale reactors fed with membrane bioreactor (MBR) effluent. The objectives were to evaluate: (i) how stagnation affects the diversity and taxonomic composition of microbial genes and proteins; (ii) how prolonged stagnation over three, five, and seven months drives temporal changes in community and functional dynamics; (iii) which functions are enriched or depleted under stagnation; and (iv) how these taxonomic and functional shifts relate to the ecological quality and biostability of reclaimed water. By understanding not only what microbes are present but also what they are doing through metaproteomics, we can assess how microbial activities impact water quality. This approach enables evaluation of treated wastewater quality both post-treatment and during distribution and storage in irrigation systems.