Consistent growth of the marine aquaculture industry over the past decades calls for potential deployments of large-scale aquaculture structures to produce finfish, shellfish and macroalgae in varying inshore and offshore environments. Numerical simulations for engineering design applications become more challenging with increase of scale since current velocity fields are no longer uniform, complicating accurate hydrodynamic load calculations. Horizontal and vertical velocity profiles in this case are spatially (depth and particular location within the deployment site) and temporary (date and time) dependent. Thus, proper representation of the current velocity field in numerical models becomes crucial for accurate predictions of structural performance of aquaculture installations. In this paper, an advanced multidimensional approximation method based on discrete current velocity data is formulated. The approach implies presenting the continuous current velocity function as a superposition of weighted radial basis functions extended by a linear polynomial. To address overfitting issues, the thin plate regularization is applied in the method. The approximation is then constrained in order to fit the velocity values on the domain boundaries. The method is implemented in finite element software Hydro-FE and its performance is compared to other approximation methods on the example of a kelp grow line deployed at the Wood Island research site, Maine, USA. It was found that the difference between regular (mean or linearly interpolated) velocity profiles and the velocity profiles approximated with the radial basis function method can reach up to 34–38 % in terms of grow line mooring tensions, and 6–18% in terms of grow line displacement.