The Mediterranean pond turtle Mauremys leprosa is widely distributed in Morocco. Significant variations could be observed in this species due to the fact that it occupies a vast and environmentally diverse area. Thus, the analysis of population parameters is crucial in elucidating the differences between populations. Differences between individuals may be linked to environmental factors, including many habitat characteristics. In the present study, variation in population structure, body condition, morphology and sexual dimorphism, were examined for the Sahara Desert blue-eyed turtle M. l. saharica in southern Morocco from seven distinct localities distributed in four different drainages in southern Morocco. A total of 224 turtles were captured, sexed, weighed and then measured for their carapace and tail dimensions before being released. Among the studied populations, four were dominated by adult individuals (Taakilt: 96%, Oued Guir: 87%, Oued Ziz: 75%, Sidi ElMehdaoui: 70%), two comprised 100% of adults (Oued Noun and Tarmigt) and one population consisted of 50% adults (Lower Draa). The sex ratio was significantly different between populations, being balanced in two populations (Tarmigt and Sidi El Mehdaoui), male-biased in three populations (Oued Zizi, Oued Noun, Lower Draa) and female-biased in the two remaining populations (Oued Guir and Taakilt). Body Condition Index (BCI, g/cm3) was significantly different among populations but not between sexes, or for the Sex × Locality interaction. The Sexual Size Dimorphism (SSD), females being larger than males, varies among population with the greatest degree observed in Oued Guir population (SSD = 0.41) and the lowest in Sidi El Mehdaoui population (SSD = -0.14). Length-Weight Relation (LWR) shows that M. l. saharica has isometric growth for both male and female of Oued Guir and Tarmigt, for female of Oued Ziz, Taakilt, Oued Noun and lower Draa and hypo-allometric for male of Oued Ziz, Taakilt, Oued Noun, Lower Draa and for both male and female of Sidi El Mehdaoui. Morphological variation of carapace is shown in this species associated with population variation among basins. Increased understanding of population characteristics and their fitness status must be considered in conservation and management action plans for the species and its habitat.