The Pemali Juana River Basin, referred to as "BBWS Pemali Juana", was formed in 2006, in line with the implementation of regional autonomy which divides tasks, authorities and powers between the Central Government and Regional Governments. Based on the Minister of Public Works Regulation No. 11A / PRT / M / 2006 dated June 26, 2006 concerning Criteria and Determination of River Basin, the management of river areas divided into river areas across countries; inter-provincial river areas; national strategic river areas; cross-regency / city river areas; and river areas in 1 (one) district / city. This division clearly provides limits on the management of river areas by the Central Government, Provincial Governments, and Regency / City Governments.
The start of the Great River Basin Organization (BBWS) itself was formed through the issuance of Minister of Public Works Regulation No. 13 / PRT / M / 2006 dated July 17, 2006 concerning the Organization and Work Procedures of the Great Basin. In the Appendix 1 table of the regulation, the type of hall of the Pemali Juana BBWS, the location of the province, and the river area are described as the Working Areas of each BBWS. This Ministerial Regulation states that the Working Area of Pemali Juana BBWS consists of the Pemali-Comal River Region and Jratunseluna River Basin.
At the organizational level, the organizational structure of BBWS Pemali Juana underwent changes after the enactment of the Minister of Public Works and Public Housing Regulation No. 34 / PRT / M / 2015 dated 1 July 2015 concerning the Organization and Work Procedures of the Technical Implementation Unit of the Ministry of Public Works and Public Housing. Through this regulation, BBWS Pemali Juana strives for optimal management of Water Resources in Central Java Province, particularly in the Pemali-Comal River Region and Jratunseluna River Basin which is its responsibility.