The objective of this study was to investigate magnesium concentrations and load, and to determine their seasonal changes in runoff water from catchments classified as nitrate vulnerable zones. The results indicate that the average concentrations of 12.2 mg Mg⋅dm-3, with fluctuations within the range of 3.3 to 26.2 mg⋅dm-3, and average annual load of 14.3 kg Mg⋅ha-1⋅year-1, with fluctuations within the range of 4.8 to 41.6 kg Mg⋅ha-1⋅year-1, in runoff water from agricultural areas are determined by weather conditions (season), type of drainage system (ditches, drains) and fertilization intensity. In comparison with land drained by a network of drainage ditches, intensive farming in drained areas increases magnesium loss 2.5-fold from 10 kg per hectare of semi-intensively farmed area to 25 kg Mg⋅ha-1 in an intensively farmed area. The highest magnesium loss was reported in the non-growing season, and around 46% of total magnesium load was leached out in the winter. The magnesium loss was minimized during harsh winters and summer draughts (to around 1.2 kg Mg⋅ha-1⋅year-1) due to a seasonal absence of runoffs.