The premise of this article is that climate effects on lakes can be quantified most effectively by the integration of process-oriented limnological studies with paleolimnological research, particularly when both disciplines operate within a common conceptual framework. To this end, the energy (E)-mass (m) flux framework (Em flux) is developed and applied to selected retrospective studies to demonstrate that climate variability regulates lake structure and function over diverse temporal and spatial scales through four main pathways: rapid direct transfer of E to the lake surface by irradiance, heat, and wind; slow indirect effects of E via changes in terrestrial development and subsequent m subsidies to lakes; direct influx of m as precipitation, particles, and solutes from the atmosphere; and indirect influx of water, suspended particles, and dissolved substances from the catchment. Sedimentary analyses are used to illustrate the unique effects of each pathway on lakes but suggest that interactions among mechanisms are complex and depend on the landscape position of lakes, catchment characteristics, the range of temporal variation of individual pathways, ontogenetic changes in lake basins, and the selective effects of humans on m transfers. In particular, preliminary synthesis suggests that m influx can overwhelm the direct effects of E transfer to lakes, especially when anthropogenic activities alter m subsidies from catchments.The structure and function of lake ecosystems is regulated by complex interactions among climate, humans, ecosystem morphology, and catchment characteristics, each of which varies in time and space (Schindler 2001). For example, climatic controls range from daily meteorological variations in local irradiance, temperature, and water fluxes (Keller 2007) through to large-scale interactions of the atmosphere and oceans (Trenberth and Hurrell 1994;Hurrell 1995;Mantua et al. 1997) and millennium-long changes in energy (E) and mass (m) flux around the planet (Williams et al. 1997;Diffenbaugh et al. 2006). Within this framework, chemical, physical, and ecological processes combine to determine the production and composition of aquatic communities, both uniquely and in consort with other mechanisms (Carpenter 1999). In addition, lakes are affected both by human disturbance of biotic communities and biogeochemical cycles (e.g., land use, urbanization, fisheries management) and by creation of novel stressors (e.g., acidic precipitation, toxicants, ozone loss). However, because these factors interact over diverse spatial and temporal scales, it is difficult to determine the relative importance of regulatory processes using only traditional site-based observation and experimentation. Instead, it is the premise of this article that the combined use of limnology and paleoecology represents the best means to quantify and scale interactions between climate and other control mechanisms and to develop a hierarchical understanding of how these regulatory processes are likely to influence lakes pres...