Reactive transport codes are widely applied in geoscience to predict or reconstruct spatial and temporal evolution of geochemical systems. To provide an accurate description of natural systems at different spatial and temporal scales, the reactive transport code has to deal with coupling of different physical and chemical phenomena. Many reactive transport codes have been developed in the past and each of these codes has specific strengths and limitations. Here, we present a new versatile reactive transport framework based on the FEniCS equations solver and the chemical solver Reaktoro. This development was motivated by the need for an advanced open-source tool allowing user-friendly modeling environment and, at the same time, full control over the numerical methods. Unlike most of the currently available codes, the developed FEniCS–Reaktoro framework offers full flexibility in setting up the reactive transport simulations of arbitrary complexity in terms of process couplings, simulation domain geometry and the boundary conditions applied. The simulations are setup using a simple high-level scripting language intuitively linked to the equation based model definition without the need of advanced programming skills. The chemical solver Reaktoro allows thermodynamic modeling of multicomponent multiphase system with several fluids and solid phases, including highly non-ideal solid solutions. The coupling of transport and chemistry is implemented using the sequential non-iterative approach (SNIA) in which the transport of the aqueous components and the chemical reactions are solved in two consequent steps. The flexibility and results of the FEniCS–Reaktoro framework are demonstrated against several widely accepted reactive transport benchmarks.