The variations in vegetation coverage (defined as the area with Normalised Difference Vegetation Index (NDVI) > 0.2) and atmospheric patterns occurring during various vegetation seasons in the Kabul River Basin (KRB) in Afghanistan during 2001–2019 were analyzed. The analysis was done based on the NDVI, land surface temperature (LST), precipitation images from the remote sensing data, and geopotential height and temperature at 500 hPa from the retrospective datasets. The results revealed that the vegetation dynamics in KRB are impacted by both precipitation and LST. In the winter season, the LST has a more substantial role in shaping the vegetation dynamics than precipitation, while it is on contrary during the summer season. Cluster analysis showed that the four atmospheric patterns (e.g., Sub-Tropical High Pressure (STHP), Western European ridge-the Eastern Mediterranean and the Black Sea trough, Caspian Sea ridge (CSR), and the Mediterranean Sea trough-Central to Eastern Iran trough) can be identified and connected with the periods with the highest and the lowest vegetation coverage (VC) anomalies in the study area. The CSR and the Mediterranean Sea trough-the Central to Eastern Iran trough are the patterns responsible for the most positive VC anomalies. At the same time, the STHP and Western Europe ridge-the Eastern Mediterranean and the Black Sea trough are responsible for the most negative VC anomalies. As the atmospheric patterns have a significant role in shaping the vegetation status, a quick alert system to prevent agricultural areas from water or temperature stresses can be developed based on observations of them.