Systems and methods for a single-difference based pre-filter of measurements for use in solution separation framework are provided. In certain embodiments, a navigation system includes at least one receiver configured to receive a plurality of signals transmitted from a plurality of transmitters. The navigation system further includes a processing unit operatively coupled to the navigation system, the processor configured to identify a plurality of measurements associated with the plurality of transmitters. Additionally, executable instructions cause the processing unit to calculate an auxiliary navigation solution based on a calculated single difference between the plurality of measurements; calculate one or more single difference residuals for the auxiliary navigation solution; perform statistical tests on the one or more single difference residuals; and to identify a set of measurements in the plurality of measurements for use in a solution separation method based on the statistical tests.