Recreational water activities are widely recognized to have a positive impact on our physical and mental well-being. However, recreational water sources and their management are also a risk factor for human health, due to different agents, including the overgrowth of cyanobacteria and algae. These organisms have the potential to metabolize organic matter and produce thermophilic and thermotolerant toxins. Different species of algae participate in biofilm formation and impact on maintenance of equipment for water treatment. We reviewed the state of the art by providing basic definitions, taxonomy and the epidemiological and clinical issues related to the recreational uses of waters. Methods for treatments and monitoring are summarized, considering both traditional and innovative strategies. Public health and surveillance perspectives impose to focus on the detection of toxins, the formation of biofilms, the understanding of the benthonic and planktonic components as part of a larger microbial biodiversity.