This is the first seasonal observation study on nutrient dynamics undertaken in a small freshwater lake with eutrophication in Mongolia. The vertical profile and seasonal fluctuation of nutrients are crucial to understanding the biogeochemical cycles in aquatic systems. In this study, field research was carried out at a small and shallow lake, Lake Bulan, in the lower Kharaa River basin. The area has been receiving increased nutrient loads from the water catchment area for the last 20 years. Water samples were collected seasonally from the lake from 2019–2022 and analyzed for nutrients, major cations, trace metals, and dissolved organic carbon. The average concentration of dissolved inorganic nitrogen (DIN) in the surface lake water had a wide seasonal variation from 0.26 ± 0.11 mg N/L in August to 1.44 ± 0.08 mg N/L in January. Seasonal differences were also observed in the vertical profiles. Concentrations were relatively similar at the various water depths in April and September at turnover time. Thermal stratification was observed when the lake was covered in ice, with the maximum concentrations being observed in the bottom layer in the months of January and August. The phosphate concentration showed a similar variation trend. These results indicate that both the summer and winter stratifications are important for regeneration of nutrients in the bottom layer, biochemical cycling, and mitigating impacts of global warming on small and shallow lakes in Mongolia.