A new ATR-IR cell was designed, and its performance was characterized by modulation excitation spectroscopy (MES). The new cell allows concentration modulation at relatively high frequency without unnecessary phase delay in the response. The response delay due to convection and diffusion was studied at different flow rates and modulation frequencies by experiments and simulations. The diffusion behavior of a small relatively fast-diffusing molecule, acetonitrile, was compared with that of a large slow-diffusing molecule, hemoglobin, in water. Experimentally, significant differences in their diffusion behavior were observed. The flow and diffusion behavior of the probe molecules was described using two different models, the diffusion layer model and the convection−diffusion model, and the theoretical results were compared with the experiments. The diffusion layer model allows estimating an effective diffusion layer thickness near the surface of the internal reflection element. However, the simulated response is significantly different from the experimental one. On the other hand, the convection−diffusion model describes the flow and diffusion behavior of the solute molecules with high accuracy. This work forms the basis for the investigation of chemical and physical kinetics such as surface reaction and diffusion by MES. It also suggests criteria for appropriate experimental conditions in ATR-IR MES experiments.