Fluctuations in the brightness of the Earths atmosphere originating from water vapor are an important source of noise for ground-based instruments attempting to measure anisotropy in the Cosmic Microwave Background. This paper presents a model for the atmospheric fluctuations and derives simple expressions to predict the contribution of the atmosphere to experimental measurements. Data from the South Pole and from the Atacama Desert in Chile, two of the driest places on Earth, are used to assess the level of fluctuations at each site.