Algal bacterial biodiversity decreased within 24 h of decay, and the environment transitioned to anaerobic conditions.

Bacterial community structure was dynamic and changed significantly with decay time.

Decomposition processes support distinct bacterial communities and promote growth of potentially pathogenic bacteria.

The abundances of enteric and potentially pathogenic bacteria increased in the Cladophora mat at 2–7 days of decay.

Understanding of the role that Cladophora plays in the accumulation and spread of potential pathogens in the Great Lakes is furthered.