The most widely used surfactant in the world, sodium dodecyl sulfate (SDS), has an inhibitory effect on environmental microbes. Since the emergence of COVID-19, more SDS has been released into natural aquatic environment through lake–terrestrial ecotone, which has had a non-negligible impact on soil microbial activities and circulation of materials in lake–terrestrial ecotones. The lake–terrestrial ecotone is also a major site for the degradation and removal of SDS. Using simulation studies and high-throughput sequencing techniques, it could be possible to determine the concentration changes in SDS in soil and water in a lake–terrestrial ecotone, as well as the variations in diversity, species composition, and functional genes in soil microorganisms before and after SDS contamination. The results showed that (1) the crucial window for lacustrine bacteria to degrade SDS was between 6 and 9 days following contamination. The SDS adsorbed to soil particles required at least 18 days to be completely removed from water, while it was mostly removed after 12 days. (2) SDS affected the lake–terrestrial ecotone differently depending on the type of plants present. The microbial community was less impacted and the recovery time was shorter in lake–terrestrial ecotones with abundant aquatic microphyte. SDS boosted microbial diversity in regions with significant vegetative degradation. (3) A lake–terrestrial ecotone’s initial microbial community structure was considerably altered by SDS contamination, and Acinetobacter and Pseudomonas increased in prominence at various times. When SDS was added, the microbiome’s ability to fix nitrogen was compromised, and the number of genes involved in nitrogen and sulfate respiration increased. The abundance of human pathogenic genes also rose dramatically.