Plateau lakes are often pristine and less disturbed ecosystems. Studying the interactions among microbial diversity, resistance genes, and nitrogen metabolism processes in these environments can provide profound insights into natural processes. This study investigated eight typical Plateau lakes and explored the distribution patterns of microbial communities and functional diversity across different fractions (pore sizes). It was found that particle-attached (PA) fractions exhibited significantly higher community diversity, while free-living (FL) fractions showed significantly higher functional diversity. Multiresistance, macrolide-lincosamide-streptogramin (MLS), and tetracycline resistance genes are the predominant types of ARGs in Plateau lakes. Mobile genetic elements (MGEs) play a crucial role in the dissemination and risk transmission of resistance genes. A total of 64 potential hosts for antibiotic resistance genes (ARGs) were identified, with Limnohabitans, Aestuariivirga, and Stenotrophomonas being the primary carriers of ARGs in both fractions. Furthermore, it was discovered that the dissimilatory nitrate reduction to ammonium (DNRA) process dominates nitrogen metabolism in Plateau lakes, indicating a potential risk of nitrogen retention. The abundance of DNRA-related genes demonstrated a strong positive correlation with ARGs. Gammaproteobacteria were identified as the main hosts for the co-hosts of DNRA-related genes and ARGs. This research significantly contributes to understanding the ecological risks posed by the interaction between microbially-driven nitrogen metabolism and antibiotic resistance in less impacted Plateau lake ecosystems.