Fully-coupled solvers have proven to be suitable and computationally efficient tools for studying surface water–groundwater (SW-GW) interactions. Most existing fully-coupled codes use the two-dimensional, depth-averaged shallow water equations for surface flows. As a result, three-dimensional (3D) flow dynamics are ignored in the surface domain, including phenomena important for the SW-GW exchange such as turbulence. Computational Fluid Dynamics (CFD) solvers allow to capture 3D information on the surface turbulent flow by solving the full Navier-Stokes equations. Consequently, they are well-suited for the study of the actual exchange flows of water and solutes across the sediment-water interface. Among the available CFD software, the open-source toolbox OpenFOAM provides a flexible modelling framework to implement user-defined, fully-coupled models for the detailed investigation of SW-GW interaction processes. Based on this CFD platform, Lee et al. (2021) developed hyporheicScalarInterFoam, a fully-coupled 3D solver capable of solving the flow and transport processes in both surface and subsurface domains as well as the interactions across their interface. Despite the potential of this new code to tackle SW-GW interactions, its application to real-world hydrogeological scenarios is constrained by limitations in boundary conditions, parameter heterogeneity and key hydrodynamic and transport processes, among others, which hinder the accurate representation of the complex characteristics of natural systems. To overcome this, an updated and extended version of hyporheicScalarInterFoam, called darcyInterTransportFoam, is presented in this paper. The new fully-coupled solver enhances the applicability of the original by introducing novel simulation features. These include internal solver updates, such as the definition of heterogeneous and anisotropic subsurface fields and the simulation of heat transfer in both domains, as well as newly implemented add-ons, including pre- and post-processing utilities and additional boundary conditions. A complete description of all the new features is provided in this paper. Moreover, the utility of darcyInterTransportFoam is demonstrated in a test case, where the SW-GW flow, solute transport and heat transfer processes are simulated in a highly conductive river-aquifer system.