Variable contributions from different lake zones (i.e. littoral, limnetic, benthic) to whole lake metabolism depends mostly on patchiness in algal and bacterial biomass, and light and nutrient availability. In terms of the organisms contributing to metabolism in each of these zones, limnetic metabolism is dominated by phytoplankton, zooplankton, and bacterial metabolism, with low contribution from epiphytes and fish. Benthic metabolism can receive great contributions from macrophytes, macro- and microalgae, invertebrates, and bacteria. Benthic metabolism is usually highest in shallow littoral zones, or in clear-water shallow lakes, in which light reaches the bottom of the lake to stimulate primary production. In dark or turbid deep lakes, primary production may be restricted to shallower waters and aerobic respiration may be reduced or non-existent in deeper waters due to the formation of anoxic deep zones.
The degree of spatial heterogeneity in metabolic rates within a lake depends on lake morphometry, catchment characteristics (e.g.  differences in land use throughout the catchment and inputs from streams), and hydrodynamic processes. For example, lakes with more intense hydrodynamic processes, such as strong vertical and lateral mixing, are more laterally and vertically homogeneous in relation to metabolic rates than highly stratified lakes. On the other hand, lakes with more developed littoral areas have greater metabolic heterogeneity laterally than lakes with a more circular shape and low proportions of shallow littoral areas.
Light attenuation occurring throughout the water column, in combination with thermal and chemical stratification and wind- or convective-driven turbulence, contribute to the vertical distribution of nutrients and organisms in the water column. In stratified lakes, organic matter and nutrients tend to be more concentrated at deeper layers, while light is more available  at shallower layers. The vertical distribution of primary production responds to a balance between light and nutrient availability, while respiration occurs more independently of light and nutrients and more homogeneously with depth. This often results in strong coupling of gross primary production (GPP) and ecosystem respiration (ER) in lake surface layers but weaker coupling at greater depths. This means that ER rates are strongly dependent on primary production in shallower layers, while in deeper layers it becomes more dependent on a mixture of organic matter from terrestrial sources and sedimentation of algae particles and organic matter produced in shallower layers. In lakes with a low concentration of nutrients in surface waters and with light penetration below the mixed layer, primary production is higher in intermediate depths, where there is sufficient light for photosynthesis and higher nutrient availability. On the other hand, low transparent polymictic lakes have higher primary production on near-surface layers, usually with a net autotrophic balance (GPP > ER) between primary production and respiration.
Laterally, heterogeneity within lakes is driven by differences in metabolic rates in the open water limnetic zones and the more benthic-dominated littoral zones. Littoral areas are usually more complex and heterogeneous, in part because of their proximity with the terrestrial system, but also due to low water volume and high sediment-to-water volume ratio. Thus, littoral zones are more susceptible to changes in temperature, inputs of nutrients and organic matter from the landscape and river inflows, wind shear mixing and wave action, shading from terrestrial vegetation, and resuspension of the sediments (Figure 1). Additionally, littoral zones usually have greater habitat complexity due to the presence of macrophytes, which serve as shelter, nursery, and feeding place for many organisms. Consequently, metabolic rates in the littoral areas usually have high short-term variability and are typically greater than limnetic metabolic rates.