We live in a rapidly changing environment, yet scientists’ understanding of the ecological consequences of wholesale changes in climate and land use is in its infancy. So too is the incorporation of this knowledge into environmental management and policy, which is so critical because both climate and land use strongly affect ecosystems and the services that they provide to society. The main goal of this research is to develop tools to measure and understand how climate and land use by themselves and as interacting factors affect lake ecosystems across scales of time and space (cross-scale interactions), even as these factors are themselves, changing. A cross-scale interaction occurs when a factor at one scale, such as agricultural land use around a lake, interacts with a factor at another scale, such as the climate of the region the lake is located within. Such interactions can lead to situations where lakes in different climatic zones respond differently to agricultural land use in their watersheds, all else being equal.