Estuarine systems, serving as crucial continuum in the land-ocean carbon cycle, play a complex and unique role in the global carbon cycle. Influenced by factors such as topography and climate, estuarine systems exhibit significant spatiotemporal heterogeneity, rendering the study of their carbon budget scale and variation patterns an essential component of regional and global carbon cycle research. Based on the mass balance principle, this study constructs an estuarine carbon budget model by monitoring input and output flows. Through obtaining seasonal carbon parameters and environmental factors from four-year surveyed semi-arid estuaries, we find coastal wetlands contribute 86.5% and 62.7% of the total input of TOC and DIC, respectively. This significant contribution highlights the critical role of wetlands as carbon sources and potential sinks within estuarine ecosystems. Moreover, our study illuminates the profound impact of hydrological variations on carbon dynamics. During flood periods, there was a dramatic increase in estuarine CO₂ emissions, ranging from 2 to 10 times the baseline levels. This observation emphasizes the necessity of considering extreme weather events and climate change impacts in estuarine carbon budget assessments. In conclusion, this study not only advances our understanding of estuarine carbon dynamics but also provides crucial insights for improving global carbon cycle models and informing coastal management strategies.