Temperature is the major driving factor of the growth and survival of aquatic organisms as it directly affects their immunity, metabolic rate, and oxygen demand. Due to ectothermic nature of aquatic animals such as fish and shellfish, body temperature fluctuates according to changes in the environmental temperature. Increasing water temperatures affect the solubility and availability of oxygen which negatively affects aerobic metabolism. However, changes in the environmental temperature above the organism's thermal threshold will increase the oxygen demand coupled with metabolic shifts as well as also reduce the feed intake and suppress their growth and immunity. Therefore, in our study, we have proposed the thermal modeling of greenhouse integrated semi-transparent photovoltaic thermal (GiSPVT) system integrated with aquaculture water pond. An analytical expression for water pond temperature (thermal energy) and electrical efficiency (electrical energy) in terms of design and climatic parameters has been derived. In this case, thermal energy obtained from the system has been utilised to heat the water pond to maintain desired temperature for aquaculture. The proposed thermal model is valid for all climatic and weather conditions. Special cases of the proposed system namely poly-greenhouse of different shapes have also been discussed. The comparison of fish production in poly-greenhouse has also been compared with the open condition. we have revealed that the production of fish in an underground tank under poly greenhouse gives about 25% higher yield during winter condition as compared to open fish production. This is due to trapped thermal energy inside the poly greenhouse and geothermal energy. Apart from this the experimental validation has also been carried out for water pond temperature.