My relationship with fish oil supplements has been long and tumultuous. As a child, I watched my father  take spoonfuls of the awfully stinky stuff and vowed to never burp up anything so foul. In my college  years I switched teams, convinced that taking a handful of fish oil pills a day would counteract all the  unhealthy things my body was being forced to endure. But recently, my work as a sustainable food  advocate has forced me to once again reconsider the nature of my relationship to fish oil.

Surely, I'm not the only person facing this paradox. The health advantages fish oil provides are well  researched and hard to overstate. However, those concerned for the health of our oceans and near  extinction of many species might think twice before purchasing any fish product. So what’s an  environmentally- but also health- conscious person to do about getting those all-important omega-3s?  What about all the vegetarians out there looking for alternative sources for those nutrients? To reach  answers to these complicated questions, let’s start at the beginning:

What is so great about omega-3s that makes this debate worth having?

Simply put, omega-3s make your body run more smoothly. The two animal-based omega-3s we receive from  fish oil supplements which have been proven to positively effect the human body are docosahexaenoic acid  (DHA) and eicosapentaenoic acid (EPA). Research has shown that these two nutrients greatly reduce risks,  and often reverse or reduce symptoms, of different types of heart disease and cancers and diabetes.  “The reason it seems able to effect so many maladies is because it’s not addressing the  condition but certain things in the body,” says Naturopath and Clinical Nutritionist David Getoff. “The  most important being helping the blood flow correctly, because if people don’t have enough omega-3s, the  blood gets thicker, and when you bring in the omega-3s, the blood starts flowing more properly—the way  it’s supposed to. Anytime our blood flows the way it’s supposed to, what could that not help?”

EPA and DHA also benefit us is by improving the permeability of the cellular membrane. “This means the  toxins can come out more easily and the nutrients, from our food or our supplements, can get in more  easily,” Mr. Getoff explains. “Again, that’s why one nutrient can help so many different conditions,  because if cells can do their job properly by having the correct permeability of the cell membrane,  which was not correct because the person was deficient in omega-3s, that makes a big difference.” Many  research scientists disagree on the proper ratio of omega-3s to the other fats we get a lot of, omega-6s  or omega-9s, for healthy adults. Most accepted ratios vary from 1:1 to 1:5. Americans, however, are  getting no where near that—depending on which research study you look at focusing on adults in North  America, the ratio varies widely from 1:14 to 1:25. So no matter what ratio you think is correct, we are  way low on omega-3s.

But don’t these pills have mercury in them?

Yes, and any amount of a toxic substance is definitely a point of concern. “We have yet to find an  amount of mercury or lead that can be looked at and it can be said that that amount is not harmful,” Mr.  Getoff says, “and there are definitely different levels of being particular when companies are working  to extract the fish oil. For example, I've called up two or three different fish oil companies and asked  to speak to their chemist to ask a number of questions. Interesting enough, my favorite brand, Carlson,  is the only company I can find that has a chemist. They check for levels of heavy metals all the time,  they make sure they are as low as they are supposed to be, if not the batch gets rejected.” Also  important to note is larger fish contain higher levels of mercury, and the older they get, the more  mercury they accumulate. Some companies such as Vital Choice, refuse to farm large fish and only farm  small fish, which have the lowest levels of mercury.

Alright, lay it on me: How do fish oil supplements affect our oceans?

The bottom line: negatively. Supplement companies source omega-3s from oily fish like salmon, mackerel,  sardines and a small fish from the herring family called menhaden. Coined “The Most Important Fish in  the Sea” by author H. Bruce Franklin, menhaden play a critical role in the aquatic food chain.  Bigger  fish that are high in omega-3s but unable to synthesize them prey on menhaden, which eat omega-3-rich  algae and clean the ocean waters off the Atlantic and Gulf coasts in the process. The menhaden helps to  prevent oxygen-depleting algal blooms that lead to underwater dead zones—in layman’s terms, they keep  our water clean. Today, menhaden are losing the battle to human consumption with hundreds of millions of  pounds a year being converted into cosmetics, paints, salad dressing and those miraculous omega-3   supplements you take.

The seriousness of the menhaden’s situation has not gone unnoticed, although steps taken to prevent its  extinction are falling short. For the last decade, Omega Protein of Houston has been catching 90 percent  of the nation’s menhaden. Realizing the excessive damage the company was causing the ecosystem, 13 of  the 15 Atlantic states have banned Omega Protein’s boats from their waters. However, North Carolina and  Virginia remain the company’s strongholds and it still maintains its right to fish in federal waters. At  present day, half a billion menhaden are fished from our oceans every year.

I don’t want to contribute to the destruction of our ecosystem! How am I supposed to get my omega-3s?

According to H. Bruce Franklin, there are numerous commercial omega-3 supplements that don’t contribute  directly to the quickly depleting population of menhaden and other fish—but it’s tricky business trying  to sort out the good from the bad. “The names of fish oil supplements are so varied and shifting that  it’s really necessary for ecosystem supporters to look at the ingredients,” says Professor Franklin,  “I've never seen ‘menhaden' listed on a label; if the product uses menhaden, the manufacturer or  distributor puts ‘herring' in the list of fish ingredients.  So if ‘herring' is on the label, choose  another brand.”

Many of alternative supplements are plant based, but unfortunately, the body doesn’t adequately use  plant based omega-3s as they exist in nature. In other words, popular vegetarian omega-3 supplements  such as flaxseed oil and rapeseed oil do not provide the same benefits as oil from animal-based  supplements. “Neither EPA or DHA molecules exist in the plant kingdom. So if somebody takes flax seed  oil, you aren’t getting the two substances for which you are taking it,” says Mr. Getoff. “What you're  doing, without realizing it, is hoping your body can convert some of those plant based ones into the  animal ones that the body needs.” Researchexamining how much of these plant omega-3s the body can  convert varies wildly (two examples hereand here). Some people can convert 10% but most can’t even do  that, which is a bummer to say the least.

But fear not! Scientists are on the case. Companies are beginning to go straight to the source—the algae  that give menhaden and other fish much of their healthy fatty acids—for sustainable omega-3 supplements.  Maryland biotech company Martek(which on December 21 announced that it is being acquired by a Dutch  corporation) farms a multitude of algal strains and about a year ago began marketing life’s DHA, an  algal omega-3 supplement rich in DHA. In November of 2010 the company announceda new blend version of  its life’s DHA and a DHA/EPA blend from algal sources. “Martek Biosciences manufactures omega-3   supplements directly from algae,” says Professor Franklin, “so their products are not only  ecosystem-friendly but also fine for vegans.” Other companies are also coming up with similar  complexes—V-pure and Devaboth make omega-3 supplements directly from algae.

While things are looking up for sustainable sources of omega-3s, you should know exactly how  best to take full advantage of whatever supplement you're taking. No matter what omega-3 supplement you  chose to take, you should also be taking a vitamin E supplement along with it. “I never put anyone an  omega-3 supplement without putting them on a vitamin E complex,” says Mr. Getoff, “When we bring in a  whole bunch of oils and we don’t make sure there’s an adequate E complex to protect those oils as they  circulate around the body, we may be taking in more things that are going to turn rancid instead of  doing their job correctly.” Mr. Getoff only recommends one brand of E for his patients-- Unique E, and  has them take one of those capsules for about every 60 lbs of body weight.

Armed with the right tools, we as consumers can make an educated decision on the healthy,  sustainable way to get our omega-3s.

It’s not easy to reconcile the idea that taking a supplement  beneficial to your body will inevitably lead to severe, damaging repercussions for our ecosystem, but  it’s the truth.

A single adult menhaden can clean four to six gallons of water in a minute, and every  year we remove half a billion of these little guys from our oceans. Menhaden are small fish with a big  role, whose future is in our hands.

After years of flip-flopping between grimacing over burps and exalting it as a miracle cure to bad  habits, in the end my relationship with fish oil boiled down to the fact that there are greener  omega-3s in the sea. I don’t have to compromise my health for the health of our ecosystem or  vise-versa. I implore you to join me in exploring other options—the voices of many sustainable food  advocates have already pushed Martek and other companies to explore varieties of oilseed-algae hybrid  options. The reality is, we're going to need to find other sources for omega-3s eventually—but the  question is whether or not we're going to do in time to save the menhaden and rescue our ecosystem.