Widespread flooding and inundation across the U.S. Midwest during spring and early summer 2019 forced many farmers to delay crop planting. New satellite observations of vegetation photosynthesis and atmospheric CO2 offer the opportunity to quantify the effects of such events on cropland carbon sequestration. We show that the delayed planting resulted in a shift of 16 days in the seasonal cycle of the crop growth and a ~15% lower peak solar‐induced chlorophyll fluorescence value. We estimate a reduction of 0.21 PgC in the gross primary production during June and July, partially compensated in August and September (+0.14 PgC). The extension of the 2019 growing season into late September is likely to have benefited from increased water availability and late‐season temperature. Ultimately, this change is predicted to reduce the crop production over most of the Midwest Corn/Soy belt by 15%, based on the strong empirical correlation between 2018 growing season SIF and crop yield. The bottom‐up estimated net carbon uptake reduction of ~0.1 PgC in June and July is consistently supported by top‐down inferred CO2 anomalies from both aircraft and satellite observations. We anticipate that such a rapid event detection can benefit agricultural and natural resource management and ecological forecasting efforts.