Information on spatial, temporal, and depth variability of soil salinity at field and landscape scales is important for a variety of agronomic and environment concerns including irrigation in arid and semi-arid areas. However, challenges remain in characterizing and monitoring soil secondary salinity as it can largely be impacted by managements including irrigation and mulching in addition to natural factors. The objective of this study is to evaluate apparent electrical conductivity (EC_a)-directed soil sampling as a basis for monitoring management-induced spatio-temporal change in soil salinity in three dimensions. A field experiment was conducted on an 18-ha saline-sodic field from Alar’s Agricultural Science and Technology Park, China between March, and November 2018. Soil EC_a was measured using an electromagnetic induction (EMI) sensor for four times over the growing season and soil core samples were collected from 18 locations (each time) selected using EMI survey data as a-priori information. A multi-variate regression-based predictive relationship between EC_a and laboratory-measured electrical conductivity (EC_e) was used to predict EC with confidence (R² between 0.82 and 0.99). A three-dimensional inverse distance weighing (3D-IDW) interpolation clearly showed a strong variability in space and time and with depths within the study field which were mainly attributed to the human management factors including irrigation, mulching, and uncovering of soils and natural factors including air temperature, evaporation, and groundwater level. This study lays a foundation of characterizing secondary salinity at a field scale for precision and sustainable management of agricultural lands in arid and semi-arid areas.