A Global Navigation Satellite System (GNSS) based navigation system with signal fault detection is provided. A least one controller is configured to; determine a true carrier phase measurement associated with each satellite signal received at each antenna of a plurality of spaced antennas; resolve integer ambiguities in true carrier phase measurement differences; and calculate at least one variable of a first navigation solution based on the obtained first set of resolved integer ambiguity measurements. The at least one controller is further configured to apply a solution separation process to repeatedly; calculate the at least one variable of a second navigation solution; determine a difference between the at least one variable of the second navigation solution and the first navigation solution; and detect a fault in satellite signals when the determined difference exceeds a defined threshold.