We consider the Boussinesq‐Peregrine (BP) system as described by Lannes [Lannes, D. (2013). The water waves problem: mathematical analysis and asymptotics (Vol. 188). American Mathematical Soc.], within the shallow water regime, and study the inverse problem of determining the time and space variations of the channel bottom profile, from measurements of the wave profile and its velocity on the free surface. A well‐posedness result within a Sobolev framework for (BP), considering a time dependent bottom, is presented. Then, the inverse problem is reformulated as a nonlinear PDE‐constrained optimization one. An existence result of the minimum, under constraints on the admissible set of bottoms, is presented. Moreover, an implementation of the gradient descent approach, via the adjoint method, is considered. For solving numerically both, the forward (BP) and its adjoint system, we derive a universal and low‐dissipation scheme, which contains non‐conservative products. The scheme is based on the FORCE‐ method proposed in [Toro, E. F., Saggiorato, B., Tokareva, S., and Hidalgo, A. (2020). Low‐dissipation centred schemes for hyperbolic equations in conservative and non‐conservative form. Journal of Computational Physics, 416, 109545]. Finally, we implement this methodology to recover three different bottom profiles; a smooth bottom, a discontinuous one, and a continuous profile with a large gradient. We compare with two classical discretizations for (BP) and the adjoint system. These results corroborate the effectiveness of the proposed methodology to recover bottom profiles.