This thesis is devoted to the derivation of a posteriori error estimates for the numerical approximation of fluids flows separated by a free surface. Based on these estimates, error indicators are introduced and adaptive algorithms are proposed to solve the problem with accuracy and low computational costs. We focus on numerical methods that are combinations of anisotropic finite elements and second order methods to advance in time. We split the technical difficulties in the derivation of the error estimates by first studying independent PDEs, and in a second time by gathering the different results to analyse the complete system of equations composed with these latter. The a posteriori error analysis for the approximation of these PDEs will be addressed in a particular and devoted chapter. The last chapter is dedicated to the study of the system describing two fluids flows. In each chapter, we focus on two main objectives. The first is a theoretical analysis and the derivation of error estimates, the second is the description and the implementation of an algorithm to adapt meshes and time steps. Finally, numerical experiments are performed to demonstrate the efficiency of the procedure.