Freshwater lakes are fundamental to human well-being, especially low-nutrient, clear-water lakes, which provide essential ecosystem services such as drinking water, recreation, cooling, irrigation, and fishing. However, such lakes are also endangered by climate change and anthropogenic activities, including watershed development, pollution, and food web alteration. Some of these anthropogenic impacts can cause a low nutrient lake to transition to a eutrophic state with dramatically reduced ecosystem services due to turbid water; frequent, sometimes toxic, cyanobacterial blooms; and hypolimnetic anoxia that can cause fish kills. Here, we will examine how watershed and climate drivers affect ecosystem structure and function in the critical headwater Sky Lakes along the Shawangunk Ridge with a particular focus on lake trophic state.