As a critical aquatic–terrestrial ecological transition zone, the lake littoral zone exhibits steep biogeochemical gradients and plays a vital role in regulating submerged microbial communities and their functions. This study aims to reveal how multi-scale environmental gradients influence microbial succession processes along desert lake littoral zones, as well as the distribution patterns of functional genes involved in carbon (C), nitrogen (N), and sulfur (S) cycling. The results demonstrated that microbial alpha-diversity in the vadose zone exhibited significant individual variability horizontally, while showing pronounced inter-group differences vertically. Horizontally, a distinct functional succession was observed from the shore to the water’s edge, with microbial potential shifting progressively from aerobic oxidative types toward anaerobic reductive types. Vertically, the root-intensive layer fostered more complex co-occurrence networks through enhanced interspecific interactions, suggesting higher functional resilience compared to other layers. Further analysis identified soil moisture as the primary environmental filter driving microbial composition, explaining 27.7% of the variation. Structural equation modeling (SEM) further elucidated that pH and Total Organic Carbon (TOC) were the key regulators of carbon fixation and sulfur oxidation genes, while Total Nitrogen (TN) dominated the distribution patterns of nitrogen cycling genes. These findings deepen the mechanistic understanding of microbial-mediated element cycling in desert lakeshore zones and provide a theoretical basis and data support for maintaining the functions of these fragile ecosystems.