The theory of Biot scatter was generalized to acoustically rough interfaces between fluids of differing densities and sound velocities by Tolstoy [J. Acoust. Soc. Am. 72, 960–972 (1982)] for the case kh≤1, k being the wavenumber and h the mean spacing between roughness elements. The present paper applies this approach to a harmonic point acoustic source in a fluid layer of thickness H and sound velocity c1, with: (1) a rigid floor with hard pebbles and (2) a soft floor of sound velocity c2≥c1 (Pekeris waveguide) with a monolayer of hard pebbles at the interface. For a ratio H/h=102 it is shown that: (a) pebbles have a marked influence on the usual coherent acoustic waveguide modes. This effect is best understood in terms of an alteration of the smooth-walled phase shift suffered by sound totally reflected from the bottom. This is particularly obvious for the Pekeris waveguide, for which the net effect on individual modes, for tightly packed spherical pebbles and for typical bottom acoustic parameters, is to increase their excitation amplitudes by factors approaching 2 near the limit of validity of the scatter theory (kh=1). (b) Pebbles may bring about the existence of a subsonic branch of the lowest mode, corresponding to a wall roughness boundary mode carried by the rough boundary. In the hard-bottomed model this branch always exists for k≥(εH)−1/2, where ε is a scattering parameter determined by the shape and volume per unit area of the scatterers. When combined with the criterion kh≤1 this condition yields a definite boundary wave passband. In the case of the Pekeris waveguide the passband is quite restrictive, being very sensitive to the ratio c2/c1; the boundary mode exists only for c2/c1≂1+δ, where δ≲0.008. For the special case c2=c1 the boundary wave is strongest and allows for an entirely subsonic mode having no analog in the smooth-walled model. The c2/c1 restriction being fairly stringent one must expect the chief practical effect of this kind of bottom roughness to be of the type (a).