Understanding the limitations of depth profiling with ion sputtering is essential for accurate measurements of atomically abrupt interfaces and ultra-shallow doping profiles. The effects of cascade mixing, sputtering statistics, ion-induced roughness, the inhomogeneity of ion beams, and sample rotation on the depth resolution of Si 8-doped, AlAs, and InAs monolayers in GaAs and an AlGaAs(5 nm)/GaAs(5 nm) superlattice were investigated. Atomic force microscopy (AFM) investigation of the ion-induced surface ripple formation on a GaAs substrate sputtered with 3 keV O2+ at angle of incidence theta=40-degrees showed that ripples form rapidly below 200 nm depth. AFM measured root mean square roughness of Si delta-doped GaAs sputtered with 2 keV O2+ was 0.8 and 2.6 nm with and without sample rotation showing that ripples play a dominant role in depth resolution degradation at shallow depth under these conditions of bombardment. Sample rotation yielded the lowest full width at half-maximum, 4.1 nm for a Si delta layer at 120 nm depth corresponding to a depth resolution DELTAZ=3.5 nm. Use of AFM enabled determination of the atomic mixing DELTAZ(m) and sputtering statistics DELTAZ(SS) components of depth resolution to be identified directly for the first time. These components were 3.1 and 1.5 nm, respectively.