Abstract The intensification of the global hydrological cycle is anticipated to increase the variability of precipitation patterns. Brackish wetlands respond to changes in precipitation patterns by regulating the absorption and release of CO2 and H2O to maintain the stability of ecosystem functions. However, there is limited understanding of how the inter‐seasonal precipitation distribution (SPD) affects ecosystem CO2 and H2O exchange compared with annual precipitation totals. Here, we conducted four consecutive years of field experiments in a brackish wetland, manipulating the proportion of precipitation across different seasons while maintaining a constant annual precipitation total. We utilized five inter‐SPD proportions (+73%, +56%, control (CK), −56%, −73%) to examine the effects of SPD on ecosystem CO2 and H2O exchange. Our findings revealed that the annual ecosystem CO2 and H2O fluxes showed a trend of decreasing with the decrease in spring precipitation distribution. Among them, the annual net ecosystem CO2 exchange, evapotranspiration, carbon use efficiency and water use efficiency were shown to be more sensitive to decrease in spring precipitation distribution and increase in summer and autumn precipitation distribution. This negative asymmetric response pattern suggests that annual ecosystem CO2 and H2O exchange is primarily governed by seasonal precipitation variability, with spring soil water–salt dynamics identified as the key driver. Therefore, this association can be explained by the fact that drought of the early growth stage exacerbates soil salinization and inhibits vegetation colonization and growth, thereby greatly impairing the annual CO2–H2O exchange capacity of brackish wetlands. Our results emphasized that the spring extreme precipitation‐induced soil water–salt conditions will greatly influence CO2 and H2O exchange in brackish wetlands in the future. These findings are crucial for improving predictions of the carbon sequestration and water‐holding capacity of brackish wetlands. Read the free Plain Language Summary for this article on the Journal blog.