Magnesium (Mg) is an essential element for plant growth and human health. Its availability and spatial distribution in soils depends on a wide variety of intrinsic and extrinsic factors. Understanding how Mg availability changes in space and time is crucial for preventing potential deficiencies. In 1987, a soil-monitoring network (FRIBO) was launched in the canton of Fribourg, Switzerland. It was based on 250 sites distributed evenly throughout the canton so as to include a large variety of soil types (Cambisols, Gleysols, Rendzinas, Regosols, Lithosols, Luvisols and Fluvisols) under three different land use types (croplands, permanent grasslands and mountain pastures). The aim of this research was to characterize the spatial and temporal variation of total and available forms of Mg in the agricultural soils of the canton of Fribourg and to discuss potential implications for Mg fertilization management. Total Mg concentration (MgT) averaged 5.5 g kg−1, with small differences between land use types. Spatial distribution of MgT showed higher values on the southern part of the study area, mostly on Rendzinas and Cambisols. Average concentrations of available Mg forms were significantly different according to extraction methods, with water extraction (MgH2O) having the lowest value (14.2 mg kg−1) followed by calcium extraction (MgCaCl2, 109.4 mg kg−1) and ammonium acetate + EDTA extraction (MgAAE, 148.7 mg kg−1). On average, permanent grasslands had significantly higher values for all Mg forms compared to croplands and mountain pastures, a result further corroborated by the analysis of spatial distribution. Intrinsic factors, such as soil type and terrain attributes, appeared to have a major influence on total Mg content, whereas available Mg forms depended mostly on extrinsic factors, such as land use type. Temporal analysis of soil available Mg forms revealed an overall increase between 1987 and 2016, especially after a land use change from croplands to permanent grasslands. In the light of the essential role of Mg for plant growth and development, as well as its critical role in animal health, the status of Mg should continue to be monitored in the FRIBO network and plant analysis should be implemented.