Background, aim, and scope Soil micronutrients are essential for plant growth and human health. Spatial variability and evaluation of soil micronutrient status are the research hotspot. The plain of northern Zhejiang Province, around Taihu Lake, China, is a key agriculture production area. With the rapid development of agriculture in Zhejiang Province, the management of soil micronutrients is of increasing concern to sustain crop productivity and human health. Soil-available micronutrients in the study region have not previously been studied in detail. Primary objective of this research was to examine the spatial distribution and evaluation of soil-available micronutrients in the arable land in this agriculturally important region using geostatistics. The controlling factors for the spatial variability of available micronutrients were interpreted. The research findings attained in the present study are of fundamental significance in providing a guideline for precise agriculture management practice and sustaining food security. Materials and methods Amounts of available Fe, Mn, Cu, Zn, B and Mo in 1893 soil samples taken from the arable land in nine counties in northern Zhejiang Province, around Taihu Lake, were measured and their spatial distribution patterns were investigated. Available Mn, Fe, Cu, and Zn were extracted with DTPA and analyzed by inductively coupled plasma-atomic emission spectroscopy. Available B was extracted with boiled water, then determined by inductively coupled plasma-optical emission spectroscopy. Available Mo was extracted with Tamm reagent and was then determined by inductively coupled plasma-mass spectrometry. Geostatistics was conducted for the data processing. Results More than 50% of the arable land were deficient in available Mo, while more than 70% had extremely low amount of available B. Amounts of available Cu, Zn and Mn were relatively high, whereas the soils are extremely sufficient in available Fe. The geostatisticical data shows that Mn, Cu, Zn, and Mo were best fit with an exponential model, while Fe and B were best fit with a spherical and linear model, respectively. Copper and Mo had strong spatial dependency, which is attributable to the effects of natural factors including parent material, topography, and soil type; Fe, Mn, and Zn had medium spatial dependency; however, B had weak spatial dependency, indicating an involvement of anthropogenic factors. Nevertheless, the six micronutrients studied all show spatial distribution trend to a certain extent. Discussion Based on the provincial classification standard of soil micronutrients and the results of the present study, regionalized management of soil micronutrients was recommended. We divided the soil micronutrients investigated in the present study into three types: Type I (Fe), Type II (Mn, Cu, and Zn) and Type III (B and Mo). Type I is sufficient, and its amount needs to be controlled; otherwise, it will be toxic to crops. Type II is enough and its amount does not need to be increased currently through micronutrient fertilization. However, Type III is deficient in substantial areas in the region studied and its cause of deficiency needs to be investigated; its availability needs to be improved to sustain the crop production and food quality. The availability of B and Mo in the north of Zhejiang Province should be regionally managed. Over the past two decades, the spatial variability of soil-available micronutrients in the study region was attributable to the soil formation factors as well as anthropogenic activities such as fertilization, cultivation, and other soil management practices. The lower available B and Mo concentrations in the arable land were apparently due to continuous cropping and intensive applications of fertilizers without adequate supply of micronutrients. The high available Fe and Mn concentrations in the soils were attributed to increasing soil acidification and relatively high soil organic matter contents. The high available Cu and Zn levels of the soils in this region were attributed to intensive utilization of animal manure as fertilizers. Conclusions Based on the provincial classification standard and the results from the present study, regionalized management of soil micronutrients was recommended. Moreover, the present study would provide an insight into understanding the basis for the development of innovative strategies for land management practices such as precision farming and environmental risk assessment. Recommendations and perspectives The research findings attained in the present study would help to improve our understanding of spatially variable availability of soil micronutrients and providing a quantitative basis for decision and policy making to develop innovative agricultural management strategies to sustain micronutrient nutrition. Further research should be conducted to elucidate the relationship between soil micronutrient and plant growth and human health.