Concerns over the sustained availability of fossil fuels and their impact on global warming and pollution have led to the search for fuels from renewable sources to address worldwide rising energy demands. Biodiesel is emerging as one of the possible solutions for the transport sector. It shows comparable engine performance to that of conventional diesel fuel, while reducing greenhouse gas emissions. However, the toxicity of products and effluents from the biodiesel industry has not yet been sufficiently investigated. Brazil has a very high potential as a biodiesel producer, in view of its climatic conditions and vast areas for cropland, with consequent environmental risks because of possible accidental biodiesel spillages into water bodies and runoff to coastal areas. This research determined the toxicity to two marine organisms of the water-soluble fractions (WSF) of three different biodiesel fuels obtained by methanol transesterification of castor oil (CO), palm oil (PO), and waste cooking oil (WCO). Microalgae and sea urchins were used as the test organisms, respectively, for culture-growth-inhibition and early-life-stage-toxicity tests. The toxicity levels of the analyzed biodiesel WSF showed the highest toxicity for the CO, followed by WCO and the PO. Methanol was the most prominent contaminant; concentrations increased over time in WSF samples stored up to 120 d.