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Towering storms, swirling clouds, and vortices are the cloud tops manifestation of complex weather systems shaping the atmosphere of Jupiter. We use observations from Juno's MicroWave Radiometer (MWR), the Very Large Array (VLA) and the Hubble Space Telescope (HST) to probe for the first time the depth and impact of weather on Jupiter. We use ammonia, the main source of opacity at radio wavelengths on Jupiter, as the tracer for the weather by fitting ammonia anomalies to the MWR brightness temperature variations. We show that the majority of the weather on Jupiter is confined to regions where the clouds are forming. Both the South Equatorial Belt and the Equatorial Zone have surprisingly shallow weather systems (P < 2 bar), and even in the North Equatorial Belt most of the ammonia variations is above the water condensation level (P ~ 6 bar). This confirms that the water condensation layer plays a crucial role in controlling the dynamics and the weather on Jupiter. However, the shallow nature of the weather cannot explain the deep-seated depletion down to 30 bar that the Juno mission has revealed. We do find three features, however, that extend below the water condensation layer: a vortex in the northern hemisphere reaching down to 30 bar, an ammonia plume down to 20-30 bars, and the signature of precipitation down to 20 bar. This work highlights the interplay of large-scale processes (vortices, plumes) and small-scale processes (storms) are responsible for shaping the atmospheric makeup of Jupiter.