Background: Early body composition changes, associated with physical inactivity and disease advancement are devastating for patient-related outcomes in predialysis chronic kidney disease (CKD), thus warranting a detailed analysis of body composition beyond conventional measures. Methods: The study included 40 subjects diagnosed with CKD; recruited between January to May 2021. Body composition was measured using the multifrequency analyzer, InBody 770. International Physical Activity Questionnaire-Short Form was used to assess physical activity. Suitable statistical analyses were performed using SPSS 21.0. Results: The mean age of the subjects was 58.68 ± 12.24 years. Sarcopenic obesity was prevalent in 62.5% of the subjects. Body mass index under identified obesity by 15% compared to percent body fat, especially in subjects with low muscle mass. The decline in a unit of estimated glomerular filtration rate (eGFR) significantly correlated with a decrease in weight (p = 0.02), body fat mass (p = 0.05), visceral fat area (p = 0.05), and phase angle (p = 0.01) with marginal changes in waist-hip ratio and extracellular water/total body water. The effect of physical activity on skeletal muscle mass was homogeneous between low and moderate levels, but significantly different from high activity level. Conclusion: Changes in fat and fluid compartment were associated with eGFR decline, whereas higher physical activity positively affected body composition.