The heating of ponds, lakes, streams, rivers, and wetlands determines their temperatures and the movement of heat creates the density structure in the water column in which organisms live and interact and in which chemical reactions occur. Temperature and thermal structure in individual lakes and flowing waters are dynamic and change daily, seasonally, and over longer time scales depending on rates of heating and cooling and the extent of mixing in the water column. This chapter provides the background to understand the contribution of meteorology and other factors, such as incoming streams, to heating and cooling. It describes the variables used in surface energy budgets, which, along with advection, are the largest determinants of heating and cooling, and illustrates how changes in these terms modify the thermal structure and mixing over diel and seasonal cycles for lakes at different latitudes. It presents the various ways in which heat budgets can be used to quantify stability and the extent of mixing, approaches for calculations, and interpretation of the resulting variables. Using examples from high-resolution instrumentation, it illustrates the dynamic nature of stratification, particularly in the uppermost layers of lakes, which has led to an improved understanding of the extent to which heat, solutes, and particulates such as phytoplankton will be redistributed over diel cycles. Illustrations include annual patterns of stratification as they depend on latitude, elevation, and lake morphometry. The chapter concludes with examples of changes in temperature and mixing dynamics during the recent period of climate change.