This dissertation focuses on the geomorphology, hydrology, and biogeochemistry of streams and lakes as coupled, interacting ecosystems in the Sawtooth Mountains, Idaho, USA. The study design used intensive field studies of several ecosystems nested within a broader comparative study of many ecosystems. Stream geomorphology was affected by lakes due to the glacial legacy of lakes and subsequent modification of water and sediment flux. Hydrologically, streams below lakes had more frequent and longer duration floods, and lakes were shown to attenuate summer floods, but not spring snowmelt floods. Biogeochemically, nutrient uptake among streams showed high phosphate and low nitrate uptake downstream of lakes. The results from these studies suggest that lakes can exert important influences on streams, both above and far below lakes, and that these modifications to fundamental stream processes may affect other attributes of stream ecosystems.