Coastal farmland along the Venice Lagoon catchment is threatened by saltwater contamination posing a serious risk for agricultural activities. A research project was recently started to understand the dynamics of salt water intrusion and soil desertification. The spatial simulated annealing (SSA) was used to optimize the soil sampling scheme in a 25 ha study area taking into account sampling constraints, the field shape, and apparent electrical conductivity (ECa) investigations as auxiliary information. The results show how the sampling procedure is able to consider the heterogeneous nature of the site.