White leg shrimp (Litopenaeus vannamei) is known as a prime aquacultural commodity in Indonesia. However, the rapid growth of shrimp farming has resulted in the widespread destruction of coastal ecosystems, including mangrove swamps. The intensification of shrimp culture has led to many other environmental problems. Integration of mangroves into aquaculture systems (IMAS) should be considered as a way to preserve the mangroves’ ecosystem as well as the sustainability of the aquaculture business by treating the influent and effluent water. This study aimed to assess the benefits, in terms of water quality, of the integration of mangroves into shrimp aquaculture. The results showed that temperature, dissolved oxygen (DO), and nitrite levels in the water significantly differed between sample sites. PCA analysis indicates that total organic matter (TOM), nitrates, nitrites, and ammonia were the principal factors in the overall water quality of the ponds. The highest pollution index was found in the super-intensive shrimp ponds (‘moderately polluted’), while the other sites, including the mangrove area, were categorized as ‘lightly polluted’. These findings suggest that the presence of mangroves may improve the quality of aquaculture wastewater, but that the pollution index still may not reach the ‘good’ category. It is therefore recommended that a wastewater treatment plant be installed to support the integrated aquaculture system.