Mangrove forests play a critical role in natural disaster resistance and provide meaningful livelihoods for local communities, especially integrated mangrove shrimp farming (IMSF) systems. Organic shrimp certification actually increases the value chains of shrimp farming in addition to ameliorating mangrove–forest management. Identifying technical issues and assessing environmental risks are the leading concerns when considering organic shrimp production certification. In this study, the technical practices of 30 households were investigated, and surface water and sediment samples were collected in the IMSF models and adjacent rivers in the Thua Duc Forest Management Board area, Ben Tre Province. Data collected from shrimp farming ponds and the environmental background were referred to both the Naturland and National Standards. The results showed that the average mangrove forest and shrimp pond ratio was 56.90:42.70 (%). Two technical issues were highlighted: (i) the use of rotenone, known as a toxin to kill undesirable fish before stocking shrimp, and (ii) annual shrimp pond regeneration causing increased pollution. The data showed that higher concentrations of TSS and P-PO43- were detected in surrounding rivers, while surface water in either IMSF ponds or adjacent rivers slightly surpassed the permissible levels of total Fe concentration. All parameters—including heavy metals; toxic and persistent parameters; oil and grease and coliforms analysed in surface water, and sediment samples—were lower than the detection and permissible levels. The results provided evidence that the IMSF’s practices and environmental characteristics were suitable for recommending the Naturland Standards. Recommendations and technical interventions for farmers are necessary to help reduce Fe levels and the safe use of rotenone in IMSF systems. An environmental quality monitoring programme at the target area should be applied when launching organic shrimp production.