Bangladesh’s aquaculture production contributes substantially to the local food security, health, economic benefits and livelihood opportunities. Sustainable seafood production relies on the adoption of Good Aquaculture Practices (GAqPs). However, the success of the adoption of GAPs depends on at least two key factors: changes in production costs and consumer’s willingness to pay. In this study, we developed a dynamic, multi-market and multi-species partial equilibrium model of the fish sector of Bangladesh (BDFish) for assessing the potential impact of safer rohu, tilapia and pangas initiatives on fish production in Bangladesh. The modeling of safer rohu, tilapia, and pangas scenarios was based on the results generated from separate production and consumption studies of this project. Applying these into the BDFish, we projected increased safer production for all the 3 species. Results also illustrate that other socio-economic scenario (i.e., changes in seafood spending/income) also play a significant role in projected sustainability of safer fish initiative in Bangladesh. The findings highlight the potential markets for safer rohu, tilapia and pangas in Bangladesh and the importance of integrating policies that create an enabling environment into the aquaculture development pathways.