Apricot concentrate production wastewater (APW), which contains significant amounts of phenolic compounds and exhibits antioxidant activity, is also a major environmental pollutant. This study aimed to recover valuable compounds from APW and mitigate its environmental impact using the supercritical carbon dioxide (SC–CO2) extraction method. Pressure and temperature variables were studied within the ranges of 8.5–31.5 MPa and 38.5–61.5 °C, respectively. A five–level central composite design (CCD) was applied to statistically analyze the interaction between experimental conditions and results. As a result of the extraction, up to 25% yield and 3.3% total phenolic content (TPC) recovery were achieved, along with a functional extract containing over 2000 mg GAE/L phenolic substances, antioxidant activity exceeding 3000 µM TE, and a significant amount of polyunsaturated fatty acids. Using response surface methodology, the optimum conditions for SC–CO2 extraction were determined to be 60 °C and 10 MPa. Toxicity values across three trophic levels, along with selected pollution parameters, were assessed before and after the extraction. Notably, following the extraction process, the toxic classification of the wastewater, as determined by the Daphnia magna toxicity test, improved from the very toxic category (Class IV) to the toxic category (Class III).