Mixing and stratification patterns in lakes are critical attributes because they are important regulators of distribution of gases, solutes and organisms. While numerous studies have focused on mixing and stratification in large lakes, the ecology and hydrodynamics of small lakes remain grossly understudied. This is critical because small lakes are far more abundant than large lakes globally. We studied a small (<1000 m2) and shallow (<0.6 m) lake with clear water and dense submerged charophyte stands located on Öland, SE Sweden, between March 25th and May 29th to investigate the thermal regimes, surface heat fluxes and stratification and mixing processes. Daytime vertical temperature differences developed in the water column ranging from 3 °C in March to 15 °C in May. Cooling of surface waters led to full convective mixing of the water column each night. The lake shallowed from March to May. The largest temperature differences were recorded in the early afternoon although wind speeds were highest at this time. The dense charophyte cover rapidly attenuated depth penetration of wind-induced mixing and radiative fluxes. Dense macrophyte stands can engineer their own environment by facilitating build-up of steep temperature and chemical gradients. This interaction should have implications for small lakes worldwide.