In an attempt to understand the dynamics of plankton populations in the world's oceans and to study the effect of environmental changes on plankton ecosystems, a case tool has been developed to enable biologists to construct arbirarily complex simulations of a closed volume of sea water over an extended period. This Virtual Ecology Workbench (VEW) enables pre-coded science modules to be plugged together using a graphical user interface, the resulting software configuration being compiled automatically into a single sequential C code. Here we discuss the characteristics of the generated code and describe a number of parallelisation strategies for speeding up the dominant "Lagrangian" components of the simulation. The parallelisation is achieved in a modular fashion using MPI, requiring minimal changes to the structure of the existing VEW system. The target platform is Fujitsu AP1000, although the code will execute on any platform supporing MPI. The parallelisation offers the potential to perform very large and detailed simulations, significantly beyond the scope of the existing sequential code.\r\n