Clarifying the concentration, major sources, and contribution differences of nitrogen in shallow groundwater in plateau lake areas with different climate types can provide a novel direction for the control of nitrate (NO3-) pollution in regional groundwater. Taking the shallow groundwater around Erhai Lake in the subtropical monsoon climate zone and Chenghai Lake in the dry-hot valley area of the Jinsha River as the research objects, using hydrochemical indexes and multi-isotope techniques (δ15N-NO3-, δ18O-NO3-, δ18O-H2O, and δ2H-H2O) combined with the stable isotope (SIAR) model; the differences in nitrogen concentration in shallow groundwater around Erhai Lake and Chenghai Lake were analyzed, the sources of NO3- were identified, and the contribution rates of each pollution source were calculated. The results showed that water quality of more than 33% and 5% of shallow groundwater sampling points around Erhai Lake and Chenghai Lake was worse than the groundwater Class Ⅲ quality requirements (GB/T 14848) of 20 mg·L-1 for nitrate nitrogen (NO3--N), respectively. The δ18O-H2O and δ2H-H2O in shallow groundwater around Erhai Lake and Chenghai Lake were parallel to the global and Chinese atmospheric precipitation lines, and a large intercept was present, indicating that atmospheric precipitation was not the major recharge source of groundwater in the two regions. The contribution rate of different NO3- sources in shallow groundwater around Erhai Lake was the highest for soil organic nitrogen (53.77%), followed by nitrogen fertilizer (21.75%) and manure and sewage (21.55%), and atmospheric deposition nitrogen (2.93%) was the lowest. Denitrification occurred in the transformation process of nitrogen in groundwater. The contribution rate of different NO3- sources in shallow groundwater around Chenghai Lake was manure and sewage (44.88%) > soil organic nitrogen (37.03%) > nitrogen fertilizer (16.17%) > atmospheric deposition nitrogen (1.92%), and nitrification occurred in the transformation process of nitrogen in groundwater. The climate type significantly affected the shallow groundwater level, altering the migration and transformation process of nitrogen, thereby affecting the nitrogen concentration in groundwater and the contribution of NO3- as the chief source. However, the major source of NO3- was not affected by the climate type; however was more affected by land use, agricultural activities, and manure treatment methods.