The Venetian canals are a heavily modified estuarine ecosystem, with two millennia of active exploitation. There is now great interest in remediation and management. The organic-rich sediments contain a mixture of fine sand, human waste, industrial wastes, and disintegrated building materials. Their microbial composition has not been well-characterized. Our goal is to build databases of microorganisms and genes in the sediments. These could guide further research into this economically, culturally and historically important ecosystem. Presented is a preliminary analysis of the organismal database.