Cayuga Lake serves as a drinking water source as well as a popular recreational lake. It is the second largest of the Finger Lakes (New York, USA), with a long narrow shape. Concerns exist regarding the lake’s phosphorus and turbidity loadings, specifically on the southern shelf (also where three point sources discharge: two waste water treatment plants and Cornell’s Lake Source Cooling Facility). Cayuga Inlet, along with Fall Creek, flow into the southern end and account for 40% of the total inflow to the entire lake. Studies indicate Cayuga Inlet and Fall Creek account for 87% of the bioavailable phosphorus load specifically entering in the southern shelf. A number of complex physical processes establish exchange and transport between the lake and the inlet. Understanding which mechanisms control transport of loadings is essential to evaluating the processes that govern water quality. Using data collected over the summer and fall months in 2015 and 2016 along Cayuga Inlet, from the inflowing tributaries, through the inlet, and out to the southern lake, we examine various physical mechanisms and their influence on turbidity loads. Velocity profiles in Cayuga Inlet are captured with an acoustic Doppler current profiler (ADCP) and High Resolution (HR) acoustic Doppler Profiler (ADP), and turbulence measures with an acoustic Dopper velocimeter (ADV). Water quality sondes are used to monitor turbidity and temperature along with a widely-distributed set of thermistors to obtain a detailed description of temperature structures throughout the area of interest. Data from United States Geographical Survey (USGS) gage stations as well as local meteorological stations are utilized to more fully understand forcing mechanisms important to flow behavior in Cayuga Inlet. Our results suggest flow through Cayuga Inlet is continuously influenced by barotropic seiches in Cayuga Lake while occasional large baroclinic events occur, the largest of which transport lake water into Cayuga Inlet. Over the stratified season exchange flows are typical and largely forced by temperature differences between the tributaries and southern lake bounding the inlet. The predominant wind stress is along the axis of the lake and the inlet and sets up seiching behavior in the lake which influences flow behavior in the inlet. A strong wind stress also increases vertical mixing in the inlet. Minimal sediment resuspension occurs in the inlet and generally, the inlet is a conduit through which suspended sediment is advected. The tributaries carry significant turbidity loads into the inlet during runoff events, which in two layer flows under conditions of cooler tributary temperatures relative to the inlet and southern lake, typically appear in the lower layer. In the spring, when the southern lake is expected to be cooler than that observed over the summer and fall deployment periods analyzed here and tributary flows are expected to warm faster, significant turbidity loads may pass through the top layer of the inlet with more frequency. At times turbidity loads in the southern lake are transported by seiching back into the inlet and again in two layer flows typically appear in the appropriate stratified layer based on the southern lake temperature relative to the inlet and tributaries.