Waveguide-enhanced Raman spectroscopy (WERS) is a promising technique for sensitive and selective detection of chemicals in a compact chip-scale platform. Coupling light on and off the sensor chip with fibers however presents challenges because of the fluorescence and Raman background generated by the pump light in the fibers; as a result all WERS demonstrations to date have used free-space coupling via lenses. We report a packaged, fiber-bonded WERS chip that filters the background on-chip through collection of the backscattered Raman light. The packaged sensor is integrated in a ruggedized flow cell for reliable measurement over arbitrary time periods. We also derive the figures of merit for WERS sensing with the backscattered Raman signal and compare waveguide geometries with respect to their filtering performance and signal to noise ratio.