At frequencies below 1 Hz, fluctuations in atmospheric emission in the Chajnantor region in northern Chile are the primary source of interference for bolometric millimeter-wave observations. This paper focuses on characterizing the statistics of these fluctuations using measurements from the Atacama Cosmology Telescope (ACT) and the Atacama Pathfinder Experiment (APEX) water vapor radiometer. We show that the total precipitable water vapor (PWV) is not in general an accurate estimator of the level of fluctuations in millimeter-wave atmospheric emission. We also show that the microwave frequency spectrum of atmospheric fluctuations is in good agreement with predictions by the am code for frequency bands above 90 GHz. We introduce a new method for separating atmospheric and systematic fluctuations, allowing us to fit a robust atmospheric flat field, as well as to study in the atmosphere in greater detail than previous works. We present a direct measurement of the temporal outer scale of turbulence of 𝜏0 ≈50  s corresponding to a spatial scale of 𝐿0 ≈500  m. Lastly, we show the variance of fluctuations in ACT’s mm-wave bands correlate with the variance of fluctuations in PWV measured by APEX, even though the observatories are 6 km apart and observe different lines of sight.