Fourteen organic dairy farms were used to (1) evaluate seasonal variation of bioactive fatty acids in milk; and (2) evaluate supplementation of ground whole flaxseed to maintain levels of bioactive fatty acid concentrations during the non-grazing season. During year round farm visits (twice a month during the grazing season and once monthly during the non-grazing season) from April 2012 until April 2015, milk, feed, and pasture samples were collected, and diet and milk production and composition recorded. During the winters of 2013–14 and 2014–15, 9 farms supplemented ground whole flaxseed at 6% of diet dry matter to half of the cows within each herd (n = 238 cows/treatment). Milk samples were collected and pooled by treatment (flaxseed or control). Data were analyzed using the MIXED procedure of SAS. A month × year interaction (P < 0.01) for omega-3 fatty acid concentrations indicated an increase beginning in April of 2014 through the end of the study. Total milk conjugated linoleic acid (CLA) concentrations were seasonal with greatest (P < 0.01) concentrations (1.32% of total fatty acids) during the grazing season. Winter flaxseed supplementation did not impact concentrations of milk fat and milk protein, or body condition score. Compared with the control diet, flaxseed decreased total milk saturated fatty acid concentrations (P < 0.01) by 3.1 percentage units, increased omega-3 fatty acid concentrations (P < 0.01) by 88%, and tended (P = 0.13) to increase total CLA concentrations (P = 0.13) by 9.0%. While flaxseed supplementation increased milk omega-3 fatty acid concentrations, minimal impacts on saturated fatty acid and total CLA concentrations indicated a greater level of winter supplementation is required to maintain concentration of all beneficial fatty acids comparable to the grazing season.