Seabed interface depths and fathometer amplitudes are tracked for an unknown and changing number of sub-bottom reflectors. This is achieved by incorporating conventional and adaptive fathometer processors into sequential Monte Carlo methods for a moving vertical line array. Sediment layering information and time-varying fathometer response amplitudes are tracked by using a multiple model particle filter with an uncertain number of reflectors. Results are compared to a classical particle filter where the number of reflectors is considered to be known. Reflector tracking is demonstrated for both conventional and adaptive processing applied to the drifting array data from the Boundary 2003 experiment. The layering information is successfully tracked by the multiple model particle filter even for noisy fathometer outputs.