Early life stages of fish are highly sensitive to crude oil exposure and thus, short term exposures during critical developmental periods could have detrimental consequences for juvenile survival. To obtain a broader understanding of the mechanisms behind crude oil toxicity, we administered crude oil to Atlantic haddock (Melanogrammus aeglefinus) in short term (3-day) exposures at two developmental time-points, before and after onset of heartbeat. A frequent sampling regime enabled us to determine and link immediate PAH uptake, metabolite formation and gene expression changes (cyp1a,b,c,d, bmp10, abcb1 and rhag). In general, the embryotoxic consequences were more severe in the earliest exposure, and oil droplet fouling enhanced the toxicity. This study detected circulation-independent, oil-induced gene expression changes and separated phenotypes linked to proliferation, growth and disruption of formation events at early and late developmental stages. A greater understanding of crude oil toxicity is essential for predicting the consequences of oil spills.Graphic abstractHighlightsOil droplet fouling occurred in the whole water column and increased the oil toxicity.Early exposure resulted in higher PAH uptake due to lower metabolism resulting in more severe abnormalities.A rapid and circulation-indepenent regulation of bmp10 suggested a direct oil-induced effect on calcium homeostasis.Expression of rhag indicated a direct oil-induced effect on osmoregulatory cells and osmoregulation.Severe eye abnormalities especially in the late exposure was linked to inappropriate overexpression of cyp1b in the eyes.