In this paper a new advection scheme for the online coupled chemical-weather prediction model Enviro-HIRLAM is presented. The new scheme is based on the locally mass conserving semi-Lagrangian method (LMCSL), where the original two-dimensional scheme has been extended to a fully three-dimensional version. This means that the three-dimensional semi-implicit semi-Lagrangian scheme which is currently used in Enviro-HIRLAM, is largely unchanged. The HIRLAM model is a computationally efficient hydrostatic operational short term numerical weather prediction model, which is used as the base for the online integrated Enviro-HIRLAM. The new scheme is shown to be efficient, mass conserving, and shape-preserving while only requiring minor alterations to the original code. It still retains the stability at long time steps, which the semi-Lagrangian schemes are known for, while handling the emissions of chemical species accurately. Several mass conserving filters have been tested to assess the optimal balance of accuracy vs. efficiency.