Science.com explains that microgravity affects the body in many different ways, primarily through bone and muscle loss. The lack of pressure on bones causes the body to reabsorb calcium from them, weakening them and potentially causing kidney stones. A similar lack of load on muscles can lead them to become atrophied over time. The body's fluids also shift, leading to inner-ear problems as well as a feeling of congestion.
Minor effects of microgravity include pressure changes inside the eye that can slightly alter an astronaut's vision, gastrointestinal distress due to changes in the digestive tract, and a slight lengthening of the spine. In addition to the direct physical changes microgravity causes in the body, other aspects of spaceflight can also have detrimental effects. For instance, astronauts deprived of the traditional day-night cycle can suffer sleep disruptions, exacerbated by the tight quarters and constant activity in spacecraft, according to the National Science Biomedical Research Institute.
In order to combat these problems, astronauts on extended space missions must make time every day for rigorous exercise programs, and must consume nutritionist planned meals in order to provide all the nutrients the astronauts need to stave off bone loss and other potentially dangerous conditions. Ultimately, astronauts must be rotated back to Earth on a regular basis to prevent long-term health issues.