Any new aquaculture venture must consider its potential to spread parasites and diseases. Where such issues exist an important consideration may be the ability to influence or change the routes by which pathogenic particles can propagate through the environment, increasing the risk to native populations. This is especially important for i) siting cultures of native macroalgae, which may affect local populations and ii) in IMTA where macroalgae must be sited near salmon pens. Using a calibrated hydrodynamic particle tracking tool, I investigate the realistic potential placement of macroalgae farms (i.e. within existing leases) and how they affect the connectivity of an entire estuary. By characterising a heavily cultivated estuary according to several metrics representing risk, I develop new configurations of macroalgae farm sites designed to reduce the risk to wild populations. Preliminary results show that targeted site selection can effectively reduce risk by altering the average risk of farm sites in the network, but that farm sites overall have little influence on the connectivity of wild populations. In this presentation I demonstrate how connectivity analysis can be a powerful tool for risk assessment and mitigation, and for optimising regulation and monitoring by identifying sites where monitoring could be most effective.