Inland water bodies serve as critical components of the global carbon cycle, yet the temporal variability of partial pressure of carbon dioxide (pCO2) introduces significant uncertainty in CO2 flux estimations. This study presents an analysis based on 38 discrete sampling events conducted between 2018 and 2024 during the ice-free period across six lakes and reservoirs in Northeast China. Measurements of pCO2 and associated water quality parameters in surface waters were used to evaluate the temporal fluctuations of pCO2 and its driving factors. The findings highlight pronounced seasonal shifts in canyon reservoirs within the study region. During spring and summer, meanpCO2 levels were recorded at 211 mu atm, indicative of a net carbon sink, with an average areal CO2 flux (fCO2) of-5.9 mmol/m2/d. However, in autumn, pCO2 levels markedly increased to 1316 mu atm, signifying a substantial carbon source, with an average fCO2 of 42.8 mmol/m2/d. In contrast, shallow water lakes exhibited relatively stable seasonal dynamics, consistently functioning as atmospheric carbon sinks throughout the ice-free period, with a mean fCO2 of-8.76 (+/- 3.74) mmol/m2/d across all seasons. Fixed-site experiments further revealed distinct diurnal fluctuations inpCO2 across different seasons, with the most pronounced daily variation (1350 mu atm) occurring in September within reservoirs. Correlation analyses between water quality parameters and pCO2 suggest that the seasonal differences in canyon reservoirs are primarily driven by the formation and breakdown of thermal stratification. Conversely, the higher nutrient availability in shallow water lakes appears to enhance CO2 uptake from the atmosphere. Additionally, diurnal pCO2 fluctuations are largely governed by variations in surface water photosynthetic activity, modulated by solar radiation. These findings underscore the importance of incorporating both stratified and mixed periods into sampling protocols, with an emphasis measurements between 10:00 and 12:00 pm, to improve the accuracy of CO2 flux assessments. This study advances the understanding of carbon cycling in temperate lakes and reservoirs and contributes to reducing uncertainties in future carbon budget estimations.