The impact of aquaculture activities has led to environmental degradation, especially ponds bottom soil quality. The purpose of this study was to assess the status of the ponds bottom ISSN 2157-6092 2016 www.macrothink.org/jee 2 soil quality in different aquaculture systems (traditional and intensive) in BLUPPB Karawang region in a flexible value of soil quality index (SQI). Twenty ponds consisting of 5 traditional of milkfish (Chanos chanos) juvenile rearing ponds and 5 traditional polyculture ponds, 5 intensive of Litopenaeus vannamei shrimp ponds lined with plastic mulch and 5 intensive L. vannamei shrimp earthen ponds. Variables of soil quality parameters examined include physical, chemical and biological of pond bottom soil. Sediment ponds with a depth of 5-10 cm were taken for analysis. Data statistically analyzed using Anova, continued with pos hoc test HSD Tukey. The results showed the ponds soil quality (SQI) of BLUPPB Karawang area has an average of 0.38 ± 0.02 or included in low criteria. Aquaculture systems were not significant (p> 5%) to the general status of ponds soil quality. Aquaculture systems (intensive and traditional) only gave a significant different (p<5%) to the parameter of soil bulk density, c-organic, total N, C:N ratio, total S, total P and soil respiration. Stability of the ponds bottom soil chemical compositions over time make level of intensity does not significantly affect, beside routine sediment removal at the end of cycle in intensive culture. Journal of Environment and Ecology