A Dynamic Energy Budget (DEB) model for the intertidal rock oyster (Saccostrea cucullata) is presented and applied for three different sites (Sonadia, Kutubdia and Inani) located in the south-eastern coast of Bangladesh, covering a distinct environmental gradient. At the three sites, field observations of oyster growth, temperature, total particulate matter (TPM) and food availability (Chlorophyll-a and Particulate Organic Matter-POM) were carried out during a period from September 2014 to August 2017. DEB model simulations produced temporal, as well as spatial variation in oyster growth as a function of the prevailing environmental conditions. Growth rates of oysters were highest (shell increment: 3 cm yr−1) at Sonadia Island due to the high food concentrations. Growth rates were relatively low (shell increment: 1.94 cm yr−1) at Kutubdia and none of oysters survived in Inani during the monsoon period. At this site TPM concentrations were quite high (889 ± 101 mg l−1), but Chlorophyll-a was quite low (1.86 ± 0.16 μg l−1) during monsoon period. Temporal variation is largely monsoon driven. The period between November to May was the main growing season for oysters along the Bangladesh coast. In contrast, growth slowed down significantly during the monsoon months (June–September). DEB model simulations for S. cucullata showed good fit (Goodness of fit score > 8.54 out of 10 and low mean relative error, MRE <0.18) with observed growth data for all three locations throughout the seasons. Therefore, the model can be used to evaluate potential sites for oyster development either for aquaculture, restoration or coastal protection to enhance coastal resilience. •DEB model for S. cucullata found useful for simulating growth in its natural environment along the Bangladesh coast.•Temporal variation in oyster growth is largely monsoon driven in the coastal areas of Northern Bay of Bengal.•DEB model can be used to evaluate potential sites for oyster culture development or restoration to enhance coastal resilience.