Organisms have evolved defense mechanisms to protect themselves from stressful conditions. The expression of heat shock proteins is considered a valid indication of protection from the adverse effects of hostile conditions. In this study, we used immunohistochemistry to investigate the seasonal effects of some abiotic factors on heat shock protein 70 and 90 (HSP70 and HSP90) expression in the liver, gills, and muscle tissues of 24 Common carp (Cyprinus carpio) caught in Karataş Lake (Burdur, Türkiye) using gillnets of various mesh sizes. We also measured some physicochemical parameters on-site at sampling time and took water samples for further analyses of other physicochemical parameters and heavy metals. Immunostaining for HSP90 was stronger than for HSP70 in both liver and gill samples. Liver and gill structures exhibited significant seasonal differences in HSP70 and HSP90 immunoreactivity, and the same was true for immunostaining for HSP70 and HSP90 in muscle samples. Some physicochemical properties seemed to vary considerably between seasons, with Fe, Mn, and Zn levels tending to exhibit changes throughout the seasons. However, these levels were considered acceptable for human health. In conclusion, this study suggests that substantial changes in HSP70 and HSP90 expression may be essential for seasonal adaptation and tolerance. Further research on fish HSPs would greatly contribute to aquaculture, which is essential for meeting food requirements.