Temperature dynamics and stratification within the water column of shallow flow-through constructed wetlands have a significant influence on their ecology and water quality. Recent research has shown that shallow water bodies are more thermally complex and more commonly exhibit complex temperature regimes than previously thought. The patterns of temperature dynamics and stratification alongside submersed macrophyte abundance and distribution were investigated in two shallow flow-through wetlands in central Iowa, USA. Sensor arrays in the water column recorded temperatures at 10-minute intervals, beginning before submersed macrophytes had become established to after submersed macrophyte senescence. Submersed macrophytes were surveyed bi-weekly using a 0.25 m2 quadrat to estimate percent cover on a per species basis. Submersed macrophyte surveys were interpolated to provide cover estimates over the entire wetland site. Complex diel temperature patterns were observed at both wetlands, with diurnal stratification followed by nocturnal mixing being by far the most common thermal regime. Increases in submersed macrophyte cover coincided with an increase in diurnal stratification. Submersed macrophyte cover appears to enhance diurnal stratification but does not significantly inhibit nocturnal mixing.