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Microwave radiometry soil moisture retrieval methods suffer from uncertainties about the representation of several effects, including dielectric mixing, surface roughness, and vegetation opacity. These uncertainties lead to two major types of error: systematic bias and random errors. The effect of the uncertainties is studied using the Soil Moisture Active Passive Algorithm Testbed, a simulation environment for evaluating error propagation in retrieval algorithms, and two different common retrieval algorithms (single and dual polarizations). The two types of errors are simulated by using different representations for each factor in the forward and retrieval parts. For both algorithms, this approach introduces a spatially variable bias, which is particularly large when using a single-polarization retrieval algorithm. This paper illustrates the emergence of both this bias and the random error due to uncertainty in the representation of vegetation and soil texture effects in retrieval algorithms. The dependence of these two types of error on vegetation and soil texture properties is shown through mapping them over the simulation region. The relative contribution of these errors to the total error is strongly dependent on the simulation conditions and is not necessarily indicative of what may be experienced during actual observations. Uncertainty due to roughness representation causes a lower error than uncertainty in vegetation opacity and dielectric mixing parameterizations in the simulated soil moisture retrieval. Summation and compensation of multiple errors can cause the estimate error to increase with improved radiative transfer knowledge, even after bias removal. The retrieval of soil moisture from microwave measurements depends on several other parameterizations that are also uncertain. This paper is limited to only three parameterizations that are considered to be among the larger contributors to bias.