Knowledge of the interrelationships between habitats and life-stage development in marine turtles requires an understanding of recruitment, size and age at maturity, sex ratios, growth and sexual development rates, survivorship and nesting probabilities. These data may be used to determine the status and survival of turtle populations during earlier life stages and for the development of appropriate conservation strategies. We sampled in-water stocks of marine turtles in coastal waters of Qatar using rodeo-style captures, entrapments in an industrial cooling intake and opportunistic bycatch to determine species, size, gender and age class. Our results revealed that Qatar is home to a resident population of small juvenile green turtles (<40 cm curved carapace length, CCL) and a transient population of juvenile hawksbills (<25 cm CCL) at an approximate 7:3 ratio of green to hawksbill turtles. Hawksbills were male-biased (4M:1F) while green turtles were slightly female biased (2M:3F). Given the extreme high ambient and water temperatures in the Arabian Gulf, which may be considered a living laboratory for understanding climate change effects on marine species, our results are not conclusive that elevated temperatures have led to feminisation of marine turtle populations. We instead believe that there may be a regional and/or evolutionary shift in the pivotal temperature that regulates ecologically appropriate sex determination, which requires further investigation. Our data provide, for the first time, a description of the foraging marine turtle population structure in Qatari waters, and point to a need for protection of seagrass beds, effective mitigation measures for sedimentation from coastal development and rehabilitation of coral-reef habitats.