During field growth, barley, triticale and oat crops can be contaminated with mycotoxin-producing fungi, posing risks to human and animal health. The aim of this study was to determine and compare the Fusarium mycotoxin content in three cereal species over two growing years to assess the impact of seasonal weather on the dynamics and intensity of cereal contamination. For this purpose, 36 barley, 22 triticale and 21 oat samples were analyzed. In both years, cereal samples were collected from the same fields in northern and eastern Croatia. Mycotoxin analysis (zearalenone, zearalenone 14-Oβ glucoside, zearalenone-14 sulfate, deoxynivalenol, T-2 and HT-2 toxin, fumonisin B1 and B2, nivalenol, 3-acetyl deoxynivalenol and deoxynivalenol 3 glucoside) was performed using liquid chromatography coupled with mass spectrometry (LC-MS/MS). Zearalenone, zearalenone 14-Oβ glucoside, fumonisins, and 3-acetyl deoxynivalenol were not detected in any cereal sample in either year. Nivalenol was not detected in barley and triticale in 2024, while T-2 and HT-2 toxins were not detected in triticale in 2025. The concentrations of other mycotoxins varied depending on the year and cereal, with deoxynivalenol showing the highest incidence, at concentrations from 22.74 to 1638.88 μg/kg. Furthermore, the results indicate a statistically significant difference (p < 0.05) in zearalenone-14 sulfate (p = 0.027) in barley and deoxynivalenol (p = 0.013) and HT-2 toxin (p = 0.014) in triticale between the observed years. Although, mean temperature and precipitation were lower in 2024 (12.6 °C and 60.71 mm, respectively) than in 2025 (13.8 °C and 68.42 mm, respectively) and these climatic factors did not differ significantly between years (p > 0.05). However, differences in mycotoxin contamination in barley and triticale may be associated with a lower mean temperature in May and June 2024 as a critical period of flowering phase with the possibility of mycotoxin formation.