A measurement system and a method for measuring a net deflection of a shaft in a wind turbine are disclosed. The measurement system includes at least one first sensor positioned proximate a first shaft component, the at least one first sensor configured to measure at least one first deflection of the first shaft component, and at least one second sensor configured to measure at least one reference deflection. The measurement system further includes a base, wherein the at least one first sensor and the at least one second sensor are coupled together and configured on the base, and a processor configured to calculate the net deflection of the shaft utilizing the at least one first deflection and the at least one reference deflection.