Several observations of Jupiter's atmosphere made by instruments on the New Horizons spacecraft have implications for the stability and dynamics of Jupiter's weather layer. Mesoscale waves, first seen by Voyager, have been observed at a spatial resolution of 11 to 45 kilometers. These waves have a 300-kilometer wavelength and phase velocities greater than the local zonal flow by 100 meters per second, much higher than predicted by models. Additionally, infrared spectral measurements over five successive Jupiter rotations at spatial resolutions of 200 to 140 kilometers have shown the development of transient ammonia ice clouds (lifetimes of 40 hours or less) in regions of strong atmospheric upwelling. Both of these phenomena serve as probes of atmospheric dynamics below the visible cloud tops.