The microstructure of green-emitting InGaN/GaN quantum well (QW) samples grown at different temperatures was studied using cross-section scanning transmission electron microscopy (STEM) and plan-view cathodoluminescence (CL). The sample with the lowest InGaN growth temperature exhibits microscale variations in the CL intensity across the sample surface. Using STEM analysis of such areas, the observed darker patches do not correspond to any observable extended defect. Instead, they are related to changes in the extent of gross-well width fluctuations in the QWs, with more brightly emitting regions exhibiting a high density of such fluctuations, whilst dimmer regions were seen to have InGaN QWs with a more uniform thickness.