The trend toward using plant‐based ingredients in aquafeeds is set to intensify; however, mycotoxin contamination might be a challenge. Two diets, with deoxynivalenol (DON) levels of 1,166 μg/kg (1.1 DON) and 2,745 μg/kg (2.7 DON), were prepared for short‐term DON exposure (50 days). A third diet with a low DON level of 367 μg/kg (0.3 DON) was prepared for long‐term DON exposure (168 days). Ingestion of DON by trout during both short‐term/high‐dosage exposure (50 days; 1,166 μg/kg and 2,700 μg/kg DON) and long‐term/low‐dosage exposure (168 days; 367 μg/kg DON) impacted growth performance and, to a lesser extent, liver enzyme parameters (2.7 DON). Histopathology showed mild to moderate changes in the liver but not in the other sampled tissues (intestine and kidney). Despite these effects, short‐term exposure of rainbow trout to high doses of DON did not result in increased susceptibility to Yersinia ruckeri. In both the short‐ and long‐term studies, the effects of DON showed a high interindividual variability. The present study confirms that subclinical levels of mycotoxins affect rainbow trout. The effects of such low mycotoxin levels could be masked by other production challenges while still negatively affecting productivity.