Taking fish oil during pregnancy has positives and negatives. Safety issues are often associated with mercury or retinol levels in fish. These substances can pass from the actual fish into fish oil supplements and, when taken by a pregnant woman, affect fetal health. In some cases, fish oil supplements contain little or no mercury or retinol, but expecting women may need to read labels carefully, or contact manufacturers, to find out total mercury content of a given product.

Fish oil is a rich source of omega-3 fatty acids. Fatty acids are typically consumed in food, but researchers have found many people have higher levels of omega-6 fatty acids in the body than omega-3s. A balance is required between these two, to achieve optimal benefits. Experts tend to support taking fish oil during pregnancy, to achieve a more balanced diet.

According to the National Institutes of Health (NIH), western diets typically contain a 15-to-1 ratio of omega-6 to omega-3 fatty acids. Health benefits, like reduced mortality, increase by 70% when that ratio is reduced to recommended levels. Increasing omega-3 consumption to reach a 4-to-1 ratio is sufficient to reduce mortality risk. For pregnant women, reaping omega-3 fatty acid benefits may require finding fish oil derived from the body flesh of fish, instead of fish liver.

Oil derived from fish liver contains retinol, which is a form of Vitamin A. Vitamin A supplementation should be avoided during pregnancy. Prenatal vitamins typically contain 8,000 IUs of it, which is the generally required level. When liver-based fish oils are consumed along with prenatal vitamins, there may be an increased risk of retinoid embryopathy.

Retinoid embryopathy is a syndrome that may cause deformation of the fetus' ears, face, and heart. Thyroid function may also be impaired by this condition. Vitamin A toxicity in pregnancy is not usually associated with beta-carotene, just retinol, so care must be taken to avoid this.

Mercury levels in fish oil supplements tend to be lower than those of fresh fish. One reason for this may be that fish oil can be cleaned, to reduce these levels, before being placed in a capsule. Women who wish to consume fish oil during pregnancy should read ingredient labels carefully. Fish low in mercury levels — like sardines, tilapia, and anchovies — normally result in fish oil with low amounts.

The human body tends to absorb fish oil during pregnancy better when fresh fish is consumed. The American Pregnancy Association (APA) suggests that pregnant women eat no more than 12 ounces (about 340 grams) of fish per week. The APA also suggests fish that should not be eaten — like tilefish, swordfish, and shark — during pregnancy due to high mercury levels. Other fish to avoid for this reason include grouper, marlin, and orange roughy.