We analysed the dynamics of Fusarium spp. and mycotoxin contamination in Swedish cereals during 2004–2018. More than 1400 cereal samples from field trials were included, collected in a monitoring programme run by the Swedish Board of Agriculture. Five Fusarium mycotoxins were quantified with LC-MS/MS and fungal DNA from four species was quantified using quantitative real-time PCR. Correlation analyses revealed that deoxynivalenol (DON) and zearalenone (ZEN) were mainly associated with Fusarium graminearum, but stronger correlations with F. culmorum was seen some years. Nivalenol (NIV) was associated with F. poae and the HT-2 and T-2 toxins with F. langsethiae. Clear differences in mycotoxin contamination between different cereal crops and geographical regions were identified. The highest levels of DON and ZEN were found in spring wheat in Western Sweden. For NIV, HT-2 and T-2 toxins, the levels were highest in spring oats and spring barley. Regional differences were not detected for NIV, while HT-2 and T-2 toxins were associated with the northernmost region. We found that delayed harvest was strongly associated with increased levels of DON and ZEN in several crops. However, harvest date did not influence the levels of NIV or HT-2 and T-2 toxins. Our results suggest similar distribution patterns of DON and ZEN, in contrast to NIV and HT-2 and T-2 toxins, probably mirroring the differences in the ecology of the toxin-producing Fusarium species. Timely harvest is important to reduce the risk of DON and ZEN contamination, especially for fields with other risk factors.