Buruli ulcer (B.U.) is an emergent, tropical and subtropical disease, causing tissue damage, large ulcers and functional disabilities in people of developing countries worldwide.  B.U. is caused by an environmental bacterium Mycobacterium ulcerans which is thought to naturally inhabit freshwater biofilms.  Although modes of transmission are not well-understood, observations suggest that B.U. outbreaks may be associated with landscape disturbance and related water quality reductions.  M. ulcerans may be associated with algae in biofilms.  Algae may alter habitats in ways that facilitate accrual of M. ulcerans, but may also directly compete with M. ulcerans for resources.  Increases in algal abundance with water quality degradation may thereby regulate M. ulcerans abundance.  We compared water chemistry parameters and cell densities and community structure of algae scraped from aquatic macrophytes from 51 sites near villages in Ghana with B.U. (endemic) or without B.U. (non-endemic) incidence.   Water dissolved oxygen concentrations were inversely correlated with the number of disease cases/village.  Algal cell densities and cyanobacteria (Phormidium, Leptolyngbya) relative abundances were significantly higher on macrophytes from endemic villages compared to non-endemic villages.  These data indicate that water quality parameters are related to disease incidence, and that environmental change may put populations at risk for B.U. infection.