The yeast Yarrowia lipolytica degrades petroleum compounds, including alkanes, via the monoterminal oxidation pathway, the hydrophobic carbon substrate assimilation is mediated by biosurfactants, and extracellular amphiphilic molecules are produced by the yeast cell. This study focuses on the ability of the strain Y. lipolytica CMGB32 to degrade n-hexadecane by producing biosurfactants with high potential for bioremediation. The hydrocarbon-degrading potential of the yeast strain was observed via a 2,6-dichlorophenolindophenol (DCPIP) test in Bushnell–Hass medium with 1% n-hexadecane, and cell hydrophobicity was expressed as microbial adhesion to hydrocarbons (MATH). Biosurfactant production on yeast peptone (YP) with 1% n-hexadecane was estimated after 72 h using the emulsification index (E24%) against toluene. Crude biosurfactant (cell-free broth) stability tests were performed at different temperatures (4 °C, 70 °C) and NaCl concentrations (2–10%). The effects of a biosurfactant on synthetic wastewater remediation comprised the growth curves (OD measurements) of natural heavy metal degrader Rhodotorula mucilaginosa, determination of nutrients (spectrophotometrically), physico-chemical parameters, and removal capacity of lead and cadmium ions (via inductively coupled plasma mass spectrometry—ICP-MS). The antimicrobial and anti-adherence activities of 20 mg/mL and 40 mg/mL of the biosurfactant against pathogenic Candida krusei strains involved growth observations and the crystal violet microtiter method. The DCPIP decolorization occurred after six days, corresponding to the maximum growth phase of the Y. lipolytica culture. After 72 h, the cells presented high hydrophobicity (82.61% MATH) and stable biosurfactant production (E24% 47%). The crude biosurfactant (5%) increased the growth of R. mucilaginosa strains cultivated on synthetic wastewater cultures contaminated with Pb2+ and Cd2+, increased the conductivity and COD (86%) of the samples, and determined Pb2+ (66%) and Cd2+ (42%) ions reduction. The concentrated biosurfactant inhibited C. krusei growth (70%) and biofilm adherence. In conclusion, Y. lipolytica CMGB32 shows important potential for development of biosurfactant-based technologies for the remediation of heavy-metal- and emerging pathogen-contaminated wastewaters.