Among the factors included in the global changes that have led to the scarcity of the sturgeon, water contamination is a growing concern. A few studies have been carried out in contexts of very high with lethal effects, but apart from that, we have very little information on the possible effects of chronic contamination on the functioning of sturgeon populations. In order to assess the tolerance of sturgeon embryos to substances widely used in agriculture, we carried out experiments with two conventional fungicides used to treat certain crops and to preserve fruit and vegetables: boscalid and imazalil. Two series of experiments were carried out with Acipenser ruthenus embryos obtained by assisted reproduction at an INRAE station, in 2021 and 2022. Experimental exposure of freshly fertilized eggs to environmental concentrations of boscalid (0.56-24.20 µg/L) or Imazalil (0.22-8.05 µg/L) was performed from the time of fertilization of eggs, to 2 days post-hatching. The results obtained highlighted that at these concentrations, there was no lethal effect and no impact on embryo hatching success, as compared to the control batch. Among the effects, we observed more precocious hatchings at the highest concentrations tested of the two fungicides and at concentrations of 0.56 µg/L, boscalid caused a reduction in the heart rate of the larvae. In addition, at the lowest concentrations, both fungicides induced abnormal growth and a change in larval swimming behaviour. Transcriptomics analyses carried out on larvae exposed to the highest concentrations of boscalid and imazalil revealed a disturbance in the transcription of genes involved in the metabolism of xenobiotics, lipids, sex steroids and mitochondria. Genes involved in development, neurotransmission and defence against oxidative stress were also altered. This study showed that at environmental concentrations, the two fungicides boscalid and imazalil affected various physiological functions and swimming behaviour in A. ruthenus larvae. These two compounds could therefore pose a risk to populations of sterlet and other sturgeon species.