Recent observations in Chesapeake Bay showed that the interaction between lateral circulation and channel-shoal bathymetry generated internal lee waves which subsequently propagated onto shallow shoals and evolved into internal solitary waves, leading to overturning and enhanced turbulent mixing. However, it is unknown under what hydrodynamic conditions the lee waves could be generated and how the nonlinear internal waves evolved. Using an idealized straight channel representative of a coastal plain estuary, we conducted numerical simulations to investigate internal wave generation over a range of river flows and tidal amplitudes. The model results are summarized using the estuarine classification diagram based on the freshwater Froude number Frf and the mixing parameter M. Δh decreases with increasing Frf as stronger stratification suppresses waves, and no internal waves are generated under large Frf. Δh initially increases with increasing M as the lateral flows become stronger with stronger tidal currents, but decreases or saturates to a certain amplitude as M further increases. This regime diagram suggests that internal lee waves can be generated in a wide range of estuarine conditions. To examine the nonlinear evolution of internal waves, a three-dimensional nonhydrostatic model with nested model domains and increasing grid resolution was configured. The lee wave steepens into a shorter elevation wave due to shoaling and soon evolves into a depression with a train of undular waves at its tail as bottom boundary mixing elevates the halocline above the mid-depth. These nonlinear internal waves enhance the turbulent dissipation rate over the deep channel and shallow shoal, suggesting an important energy source for mixing in stratified coastal plain estuaries. In addition, a pH sensor deployed at the middle reach of Chesapeake Bay recorded high-frequency variability in bottom pH driven by along-channel winds. Though wind-driven lateral circulation can advect high pH water downward, the slow air-sea exchange of CO2 limits the lateral ventilation. With DIC and TA budget analysis and comparison with cross-sections at upper- and lower-Bay where strong lateral circulation was confined in the surface layer, we found vertical mixing and replenishment of oceanic water by longitudinal advection could be more important mechanisms to ventilate bottom pH.