We introduce a novel approach to reveal ordering fluctuations in sheared dense suspensions, using line scanning in a combined rheometer and laser scanning confocal microscope. We validate the technique with a moderately dense suspension, observing modest shear-induced ordering and a nearly linear flow profile. At high concentration (ϕ = 0.55) and applied stress just below shear thickening, we report ordering fluctuations with high temporal resolution, and directly measure a decrease in order with distance from the suspension’s bottom boundary as well as a direct correlation between order and particle concentration. Higher applied stress produces shear thickening with large fluctuations in boundary stress which we find are accompanied by dramatic fluctuations in suspension flow speeds. The peak flow rates are independent of distance from the suspension boundary, indicating that they likely arise from transient jamming that creates solid-like aggregates of particles moving together, but only briefly because the high speed fluctuations are interspersed with regions flowing much more slowly, suggesting that shear thickening suspensions possess complex internal structural dynamics, even in relatively simple geometries.