This study was conducted to investigate the relative abundance and habitat analysis of freshwater turtles of Pakistan. Eighty two individuals of seven species of turtles at sixteen different sites in River Indus and some of its tributaries in Khyber Pakhtunkhwa (KP) and Punjab were recorded; these include both soft and hard shell freshwater turtles. The species documented were, Kachuga smithii, Kachuga tecta, Geoclemys hamiltonii, Aspideretes gangeticus, Aspideretes hurrum, Chitra indica and Lissemys punctata. The L. punctata was the most common, with relative frequency (RF) of 24.4%, followed by A. gangeticus (18.3%), A. hurum (17.1%), C. indica (17.1%), K. smithii (12.2%), K. tecta (7.3%), and G. hamiltonii (3.7%). It was also discovered that District Swabi was the most populous area with three densely populated sites; Yar Hussian stream, Allah Dher River and Badri stream. In order to know the habitat preferences the biotic and abiotic factors of water bodies within the freshwater turtle’s habitat (16 study sites) were also measured. Abiotic factors viz. pH ranges from slightly acidic to basic (6.90-9.43), total dissolved solids (0.28-5.07 mg/L), conductivity (7.33-26.33 mv), dissolved oxygen (0.67-16.40 mg/L), temperature of air (20°C - 40°C) and temperature of water (19°C - 34°C) were recorded. Besides, biotic components including, twenty seven genera of Phytoplankton and sixteen genera of Zooplanktons were also observed in study area.