Molecular techniques are emerging as a rapid and powerful approach for microorganism detection. This project reviewed the efficacy of PCR assays for Cryptosporidium, Microcystis, adenovirus and ammonia oxidising bacteria, as well as candidate techniques for DNA extraction and inhibitor removal. The literature review led to an evaluation of DNA extraction kits and reagents for PCR; finalisation of assay formats; the development of PCR controls and Standard Operating Procedures (SOP); analysis of assay robustness using real samples; and completion of an Inter-laboratory trial using the SOP's developed. This book is co-published with Water Research Australia.