This research studies the acute toxicity of real contaminated soils (topsoil and subsoil) with hazardous chlorinated organic compounds (COCs) from lindane manufacturing wastes. The Microtox® bioassay was used to determine the toxicity of soils (modified Basic Solid Phase Test), soil elutriates (Basic Test), and organic extracts (adapted Organic Solvent Sample Solubilization Test), in which hydrophobic organic compounds are soluble. The acute toxicity of these persistent contaminants (hexachlorocyclohexanes, HCH isomers, as particulate matter in topsoil, and COCs, from dense non-aqueous phase liquid, DNAPL, in subsoil) and the commercial compounds were also measured. Soils tested showed different contaminant levels (topsoil: 0.9–1149 mg/kg and subsoil: 20–9528 mg/kg). Soil contaminants distribution, concentration and acute toxicity were highly related to the contamination source (HCHs or DNAPL). Soils, organic extracts, and subsoil elutriates presented high toxicity, highlighting the need for remediation of these sites. EC50 was calculated in the three-test applied for the soils tested. EC50 vs. COCs concentration in soils and soil elutriates showed an asymptotic trend, explained by the low pollutants solubility in the aqueous phase. Contrarily, EC50 vs. soil COCs concentration was more linear in the case of the organic extracts. This test was the most reliable from statistical analysis. The three methods reveal interesting and complementary information and are necessary for a complete overview of the acute toxicity of contaminated soils.