The uncertainty of electron density and temperature fluctuation measurements is determined by statistical uncertainty introduced by multiple noise sources. In order to quantify these uncertainties precisely, a simple but comprehensive model was made of the noise sources in the MST Thomson scattering system and of the resulting variance in the integrated scattered signals. The model agrees well with experimental and simulated results. The signal uncertainties are then used by our existing Bayesian analysis routine to find the most likely electron temperature and density, with confidence intervals.In the model, photonic noise from scattered light and plasma background light is multiplied by the noise enhancement factor (F) of the avalanche photodiode (APD). Electronic noise from the amplifier and digitizer is added. The amplifier response function shapes the signal and induces correlation in the noise. The data analysis routine fits a characteristic pulse to the digitized signals from the amplifier, giving the integrated scattered signals. A finite digitization rate loses information and can cause numerical integration error.We find a formula for the variance of the scattered signals in terms of the background and pulse amplitudes, and three calibration constants. The constants are measured easily under operating conditions, resulting in accurate estimation of the scattered signals' uncertainty. We measure F ⇡ 3 for our APDs, in agreement with other measurements for similar APDs. This value is wavelength-independent, simplifying analysis. The correlated noise we observe is reproduced well using a Gaussian response function. Numerical integration error can be made negligible by using an interpolated characteristic pulse, allowing digitization rates as low as the detector bandwidth. The effect of background noise is also determined.