Interannual variability on metabolic rates can be driven by extensive changes in the catchment or by directional and cyclical climate change and climate disturbances, such as the events associated with the El Niño Southern Oscillation (ENSO). Those changes in the catchment, air temperature, and precipitation between years affect metabolic rates by altering nutrient and organic matter inputs to the lake, light attenuation, mixing dynamics, and by direct temperature-dependence of metabolic processes.
The increase in precipitation increases external loading of organic matter, nutrients and sediments in lakes. Moreover, increased discharge events promoted by increased rainfall can also alter mixing dynamics and cause physical flushing of organisms. While lower precipitation associated with high evaporation rates also affects limnological conditions by reducing the water level and thereby increasing the concentration of nutrients and chlorophyll, as well as changing the thermal stability of aquatic environments. During warmer years, a stronger water column stability limits the inputs of nutrients and organic matter to the photic zone. In contrast, during colder years, a less stable water column enhances resuspension of the sediments and the inputs of nutrients and organic matter from deeper waters. This lowers light availability, while enhances nutrient and organic matter availability. Thus, the effects of differences in precipitation and temperature between years in metabolic rates will depend on the intensity and duration of these changes, and also in which factors are limiting GPP and ER in each water body.
In lakes with nutrients and organic matter limitation of GPP and ER, wetter years can enhance GPP and ER rates, due to higher inputs of nutrients and organic matter from the landscape. This will depend if the terrestrial inputs will be promptly available for the primary producers and heterotrophic communities or if it is going to enter the lake through deeper waters, in which metabolic processes are very low or non-existent. In this case, the inputs will only be available in the next water column mixing event. Thus, increases in metabolic rates due to rainfall depend also on the stratification and mixing dynamics, hydrology, and morphometry of the lake. On the other hand, drier years can also have enhanced GPP and ER rates if it is accompanied by lower water levels, which would lead to higher nutrients and organic matter concentrations. A lower water level is associated with a less stable water column and higher proximity with the sediments, thus increased inputs of nutrients and organic matter from deeper waters. Also, a reduction in water level through water evaporation leads to a concentration effect. In turn, during warmer years the water column is more stable, and the depth of the mixing layer is shallower, thus reducing internal inputs of nutrients and organic matter to the mixed layer. Metabolic rates, in this scenario, will be lower in the upper mixed layer. In lakes with a photic zone extending deeper than the mixed layer, metabolic rates will be higher in intermediated depths, coinciding with the deep chlorophyll maxima.
In lakes with primary production limited mostly by light availability, increases in rainfall could lead to lower light availability, associated with increased dissolved organic matter and total suspended matter. Consequently, increased rainfall would be associated with lower levels of GPP, which would reduce respiration rates associated with autochthonous production, leading to a decoupling of GPP and ER rates. In addition, increased allochthonous organic matter availability during wet years can lead to higher ER, and consequently leading the metabolic balance to be negative (NEP <0).
Changes in annual precipitation can also affect the spatial variability in metabolic rates within lakes. Williamson and collaborators, for example, found that, in a hyper-eutrophic reservoir in North America, the relative spatial variability in GPP and ER rates were higher in a dry year compared to a wet one. These suggest higher relevance of internal processes, such as internal loading, nutrient uptake,  sedimentation, and resuspension, to metabolic rates during dry years.