In many cases accretion proceeds from disks onto planets, stars, white dwarfs, and neutron stars via a boundary layer, a region of intense shear where gas transitions from a near-Keplerian speed to that of the surface. These regions are not susceptible to the common magnetorotational and Kelvin–Helmholtz instabilities, and instead global modes generated by supersonic shear instabilities are a leading candidate to govern transport in these regions. This work investigates the dynamics of these systems under a range of thermodynamic conditions, surveying both disk sound speeds and cooling rates. Very fast and very slow cooling have little effect on wave dynamics: In the fast-cooling limit, waves propagate in an effectively isothermal manner, and in the slow-cooling limit, wave propagation is effectively adiabatic. However, when the cooling timescale is comparable to the wave period, wave damping becomes extreme. In cases with intermediate cooling rates, mass and angular momentum transport can be suppressed by orders of magnitude compared to isothermal and uncooled cases. Cooling in accretion disks leads to a preference for wavenumbers near and below the Mach number of the disk; the corresponding lower frequencies can (in nonisothermal systems) couple to gravity modes within the star, potentially driving low-frequency variability such as dwarf nova and quasi-periodic oscillations in accreting systems.