Water pollution resulting from coastal development, industrial waste and agriculture has a negative impact on sea turtles and their habitat.

Land clearing for developments and agriculture results in increased sedimentation in off shore waters. Plants and other organisms that use sunlight to generate food (photosynthesise) are less able to grow in waters with high levels of sedimentation as less light reaches them through the water column. In extreme cases sedimentation will completely smother all organisms in an area. Sea turtles that feed on seagrasses and coral reefs are affected when sedimentation slows growth or smothers their food sources.

Nutrients such as phosphorus, nitrogen and potassium from agriculture, sewerage discharge and industry washes into marine waters and creates algal blooms that damage seagrass beds and coral reefs.

Many green turtles around the world, including Australia, have contracted a potentially deadly disease called Fibropapillomatosis. This disease results in tumours that, although benign, can result in death if they grow over vital internal organs or around the eyes and throat. A reduction in resilience to disease brought on by many factors including reduced water quality are thought to lead to greater instances in cases of  Fibropapillomatosis amongst sea turtles.