Introduction Diabetes is one of metabolic diseases. In the patients with diabetes, glucose uptake is decreased and fbroblast growth factor 21 (FGF-21) plays an important role in glucose uptake. Also, Sirtuin 1 (SIRT1) is a protein regulating glucose and fat metabolism. Therefore, this study was performed to determine the efect of 12 weeks of exercises in water on serum levels of SIRT1 and FGF-21, glycemic index, and lipid profle in women with type 2 diabetes. Materials and methods For this purpose, 40 women with type 2 diabetes (with mean age of 43 years old and body mass index (BMI) of 31 kg/m2) were randomly divided into control (n = 20) and experimental (n = 20) groups. The exercise program was performed in water for 12 weeks, with an intensity of 45–65% of maximum heart rate. Blood samples were used for pre-test and post-test to evaluate serum levels of SIRT1 and FGF-21, glycemic index, and lipid profle. Then, data were analyzed using paired-samples t-test and independent-samples t-test at signifcance level of p < 0.05. Results The results of statistical analysis showed that the water exercise program signifcantly increased serum levels of FGF-21, SIRT1, and high-density lipoprotein cholesterol (HDL-C) in women with type 2 diabetes. In contrast, this type of exercise signifcantly reduced resistance to insulin, glucose, insulin, total cholesterol, triglycerides, and low-density lipoprotein cholesterol (LDL-C). Conclusion Based on results of the present study, it seems that exercise in water may play an efective role in glucose homeostasis and reduction of body fat mass, by increasing levels of SIRT1 and FGF-21 and it should be considered to prevent from development of type 2 diabetes. It can also be used as a type of exercise recommended by sports and health professionals in these people.