The proper delineation of site-specific management zones is very important in the agricultural land management of potentially degraded areas. There is a necessity for the development of prospective tools in management plans to correctly understand the land degradation processes. In order to accomplish this, we present a pedo-geomorphological approach using soil texture, land elevation and flow vector aspects to distinguish different management zones and to discretize soil micronutrients. To achieve this goal, we conducted the study in the Neyshabur plain, Northeast Iran. For data collection, grid sampling (500 × 500 m) was used with 70 specific points. Soil samples were collected in triplicates from various sites as composite samples (0–30 cm) to analyse clay, Zn, Mn, Cu and Fe. Using the altitude information (obtained with GPS at each sampling point), flow vectors were also modelled for all selected points. Based on the values of altitude, flow vectors and clay, management zones were delimited using geographic information systems. The best data organization was obtained from the combination of clay + elevation + flow vector attributes, generating two different management zones. In this circumstance, the lowest fuzzy performance index (FPI) and modified partition entropy (MPE) values were generated. It can be observed that the management zone 1 (MZ1) is located in the areas with a lower elevation and higher content of clay. On the other hand, the MZ2 was characterized by areas with a higher elevation and lower clay content. This study concluded that the design of management zones, using pedo-geomorphological information could reduce the time and cost of sampling necessary to assess potentially degraded areas of land.