To examine the deleterious effects of the water accommodated fraction (WAF) of crude oil, the growth curve, fecundity, and lifespan of the monogonont rotifer (Brachionus koreanus) were measured for 24 h in response to three different doses (0.2×, 0.4×, and 0.8×) of WAFs. A higher dose of WAFs significantly reduced the fecundity and lifespan. A rotifer 32K microarray chip showed that the Bk-CYP3045C1 gene had the highest expression. Of the 25 entire CYP genes, the Bk-CYP3045C1 gene showed a significant expression for different doses and times in response to WAFs and chemical components of WAFs (naphthalene and phenanthrene); also, glutathione S-transferase genes, ABC transporter, and other genes showed dose responses upon exposure to 80% WAF over time. Different doses of WAFs increased the oxidative stress with an induction of reactive oxygen species (ROS) and a depletion of glutathione (GSH). Exposure to WAFs did not show toxic effects on survivability in B. koreanus; however, toxicity to WAFs was shown when piperonyl butoxide, a potent inhibitor of cytochrome P450 (CYP) enzymes, was added. This toxicity was dose-dependent. After WAFs exposure, p-ERK was activated over time in response to WAFs, which suggests that WAFs can be activated by the p-ERK signaling pathway.