In this work, we consider the estimation of temperature profiles along the pipes of a plate heat exchanger. The transport phenomena through the heat exchanger are modeled by hyperbolic partial differential equations (PDE) of first order in time and space. The counterflow heat exchange implies that the system is comprised of rightward (where the hot fluid circulates) and leftward (cold fluid pipes) hyperbolic PDE. The heat exchanged between the pipes of hot and cold fluid induces a coupling between the rightward and leftward equations, which increases the difficulty of solving the PDE system. The estimation objective is addressed by the design of an observer using a PDE approach, which uses boundary measurements to estimate the distributed profiles. The convergence of the observation error is established using Lyapunov analysis. Simulation results illustrate the efficiency of our method using a simulator with time-varying parameters validated on experimental data.