There are certain species of algae that secrete harmful toxins into the water-body. But are there some of these species that can be harnessed for bio-energy synthesis?
Microcystins are a type of toxin usually produced by cyanobacteria (blue-green algae). These organisms are studied for biofuel production, especially since they can be genetically modified more easily than eukaryotic microalgae. I know some genera like Anabena produce toxins and those have been looked out for biofuel production. I would check out which organisms produce toxins and then see if anyone has does studies on them for biofuel/ bioenergy production. I wouldn't be surprised if there are some.
Algal toxins and algal fuels are completely different. Algal oil, which is used for biodiesel production is safe. If the oil contains some toxins, that may cause harm, if after their combustion their action does not get cut down. Bioethanol and biogas are produced by the microbes as byproducts. So, the chance of the spread of toxins is less in this case too because they feed on algae and these fuels are not the direct product of algae. I have done some work on algal biofuel irrespective of their species. If you are interested please find the file attached.