This paper presents our collection methods, laboratory protocols and findings in respect of sewage pollution affecting seawater and marine organisms in Table Bay, Cape Town, South Africa, then moves to consider their implications for the governance of urban water as well as sewage treatment and desalination. A series of seawater samples, collected from approximately 500 m to 1500 m offshore, in rock pools at low tide near Granger Bay, and at a depth under beach sand of 300-400 mm, were investigated for the presence of bacteriological load indicator organisms including Escherichia coli and Enterococcus bacteria. A second series of samples comprised limpets (Patella vulgata), mussels (Mytilus galloprovincialis), sea urchins (Tripneustes ventricosus), starfish (Fromia monilis), sea snails (Tegula funebralis) and seaweed (Ulva lactuca), collected in rock pools at low tide near Granger Bay, and sediment from wet beach sand and where the organisms were found, close to the sites of a proposed desalination plant and a number of recreational beaches. Intermittently high levels of microbial pollution were noted, and 15 pharmaceutical and common household chemicals were identified and quantified in the background seawater and bioaccumulated in marine organisms. These indicator microbes and chemicals point to the probable presence of pathogens, and literally thousands of chemicals of emerging concern in the seawater. Their bioaccumulation potential is demonstrated.In respect of proposed desalination, the findings indicate that desalinated seawater must be subjected to treatment protocols capable of removing both bacterial loads and organic chemical compounds. The terms of reference for desalination plants must specify adequate testing and monitoring of chemical compounds as well as microorganisms in the intake and recovered water. Drinking water supplied by the proposed seawater desalination plants should be carefully tested for its toxicity.In respect of water management, our findings suggest the need for the City of Cape Town to move to an integrated water and sewage management plan that treats urban water, including seawater, as a circulating system that is integral to the health of the City, and which excludes marine outfalls.