Lots of Small and Medium Enterprises uses natural dyes on their Batik process in Jakarta. Palbatu Tebet Batik village has applied Batik process with natural coloring but there is not any treatment center for the natural coloring waste. This causes environmental pollution and endangers the health of residents around there. Palbatu Batik Village requires wastewater treatment center. This research is implemented by making correlation between wastewater value and WWTP system. The highest BOD and COD value in the Natural Coloring process is 2870 mg/L and 8345 mg/L. Both of these values exceed the quality standards set by the government which are 75 mg/L and 100 mg/L. This research is to find out the right WWTP system to treat waste to meet quality standards. Of the several WWTP systems, only the Aerobic-Anaerobic system can reduce the BOD value to 5.166 mg/L and the COD value to 91.79 mg/L. The space requirements for the Aerobic-Anaerobic system are Fat Seperator, Equalization, Initial Sedimentation, Anaerobic Biofilter, Aerob Biofilter, Final Sedimentation, and Chlorination.