Understanding the transport processes in lakes and other aquatic systems is vitally important since much of the living biomass is transported by the water, along with nutrients, contaminants, suspended particles, and other materials important to biogeochemical processes. The hydrodynamic processes therefore determine the environmental conditions that affect the biogeochemistry. The physical processes that control the hydrodynamics of large lakes are complex, and depend on a balance of characteristics of the lake (geometry, stratification, etc.) and forcing conditions (meteorological, hydrological) that change over various spatial and temporal scales. Using data from several extensive field campaigns, including measurements of velocity and thermal structure at multiple locations over several seasons, an extensive set of CTD data, and a 15 year long bi-weekly water quality dataset at multiple locations, we analyze the physical forces controlling the dynamics of a large, narrow and deep lake, and the response of the lake to these forces. The study site is Cayuga Lake, the second largest of the Finger Lakes of central New York State, USA (latitude 43N). It is a long (60 km), narrow (less than 6 km) and deep (maximum 130 m) lake. The bathymetry at the south end of the lake slopes up to a shallow shelf, not unlike a coastal estuary, which receives discharges from both natural and anthropogenic sources, and on which sharp spatial and temporal gradients in water quality exist. The geometry of the lake and the prevailing winds in the region lead to the generation of large amplitude internal waves, which develop to be highly nonlinear. Shoaling of these waves on the southern shelf are shown to lead to the intermittent upwelling of hypolim- netic water on to the shelf, creating sharp spatial gradients in water quality (e.g., TP and chlorophyll-a concentrations) on the shelf. We analyze the internal wave field of the lake and the nonlinear processes associated with it, and the factors that lead to the sharp spatial gradients observed on the shelf. We show that a subtle balance of forces controls mixing and transport in the various regions of the lake and propose an explanation for a persistent anomaly in chlorophyll-a concentration observed in one region of the lake.