Spatial flow variance has a strong control on sediment transport, sediment-water interface exchange mechanisms, and the distribution and behavior of aquatic organisms in rivers. Thus, being able to quantify spatial flow variance, and how it varies with different water levels, is important for understanding how fluvial processes change during periods of time varying flow. In this paper, laboratory flume measurements of near-bed flow velocity were used to quantify spatial flow variance and form-induced stress, and their variation with flow submergence, within and above the surface of porous, gravel beds with differing grain roughness. The analysis revealed spatial flow variance was usually four or five times higher within the roughness layer than above. A rise in relative submergence resulted typically in a decrease in spatial variance—relative to bed shear velocity—in streamwise form-induced intensity, streamwise turbulence intensity, and form-induced momentum flux, both within and above the roughness layer. Flow submergence had no consistent influence on spatial variance in the vertical flow direction and in Reynolds stress. Form-induced stress was significant within the roughness layer, more so at shallow depths. The greater significance was driven primarily by higher spatial flow variance in time-averaged streamwise velocity at these depths. The implication is the relative role of momentum transfer mechanisms within the roughness layer, and thus, sediment-water interface exchange processes in rivers will change during periods of time varying flows.