Ensuring drinking water safety is one of the top priorities in public health. Microbial contamination in drinking water is a particular concern in China and a comprehensive monitoring of the drinking water microbiome is necessary. However, traditional culture-based monitoring methods have limitations and the nationwide water monitoring in China requires considerable investments. Here, we used a cost-effective citizen science approach to collect 50 household drinking water samples from 32 administrative regions in China. We efficiently extracted microbial DNA from low-biomass tap water and performed high-throughput Illumina sequencing of 16S rRNA genes to profile total water microbial communities and waterborne pathogens. We explored the spatiotemporal patterns of microbial communities and the influences of extreme weather events. 7635 Amplicon Sequence Variants (ASVs) were identified from 22 tap water samples including 20 normal samples and 2 weather samples collected after 7.20 Zhengzhou Rainstorm and Typhoon In-Fa in 2021. The overall microbial community compositions were found to be region-dependent and significantly driven by outdoor temperatures. The consistencies in results with previous studies suggest that the citizen science approach in this study was applicable and reliable to a large extent. Alertly, pathogenic bacteria including Mycobacteruim spp., Acinetobacter spp., and Legionella spp. were detected in all the samples. More pathogen species such as Salmonella enterica and Aeromonas hydrophila were found in weather samples while high outdoor temperatures were positively correlated with pathogen abundance. This suggests the need of extra drinking water treatment during/after extreme weather events and hot weathers in this era of climate change.