This report presents results from Wallis Lake, one of the estuaries selected as part of Stage 1, the NSW Oyster Industry Transformation Project 2017-2021. To predict the impact of rainfall on potentially pathogenic bacteria, Harmful Algal Blooms (HABs) and oyster disease, precise environmental data with a high temporal frequency were collected and modelled. Combined with state-of-the-art molecular genetic methods, this information will help to improve efficiency and transparency in food safety regulation, provide predictive information and provide insights for more informed and responsive management of shellfish aquaculture.