Due to the appearance of intensive livestock-rearing systems since the 1970s, a vast amount of liquid manure (slurry) has been produced. The application and utilization are partly regulated for this special substance, which contains urine, excrement, process water, and other chemicals, such as insecticides and disinfectants. Our research was conducted on a slurry management system of a dairy cattle farm, focusing on the investigation of the presence of oestrogenic substances and toxicity of slurry before and after using a separator technology. Yeast oestrogen screen shows in this study that the separation of the liquid and solid phases of slurry contributes to the reduction in oestrogenic substances. Based on the toxicological studies, the growth inhibition of algae was 93%, and the inhibition of the germination of higher plant seeds was 25%, without separation. After separation of the phases, growth and germination were comparable with the negative control; moreover, some stimulation was detected. Consequently, harmful substances were removed with the suspended solid phase. From the present study, we can conclude that stakeholders should support separation technology in intensive livestock-rearing systems, and ecotoxicological investigations obviously help the risk management of slurry utilization. To our best knowledge, this is the first paper presenting detailed and complex toxicological study on slurry samples.