First applied researches on related to soil and water relations came up with the emergence of problems caused by irrigation at Çukurova Irrigation Network in our country. Regional Aqueous Agricultural Experiment Stations were established in order to investigate the soil and water relationship, determine suitability of the various infrastructures required by the irrigated farming to Turkey's conditions and teach irrigated farming techniques to farmers.

The first Aqueous Agricultural Experiment Station was established in Tarsus in 1947. Increasing investments on soil and water resources also increased the number of Aqueous Agricultural Experiment Stations.Tokat Regional Aqueous Agricultural Experiment Station started its studies in 1963, covering the vast area of Tokat, Amasya, Sivas and Yozgat.With the implementation of the  "Organization and Duties of the General Directorate of Rural Services" legislation dated 9 May 1985 No:3202 continued its services under the General Directorate of Rural Services. With the closure of the General Directorate of Rural Services on 14 March 2005, our organization was renamed as 'Soil and Water Resources Tokat Research Institute' under the Agriculturel Research Directore until 2011. With the establishment of Ministry of Food, Agriculture and Livestock, our institution name changed as Middle Black Sea Transitional Zone Agricultural Research Station and continues its operations.​