Primary production informs about the organic input and oxygen production in a water body.Both parameters are important in determining the quality of marine waters or the potential for a rich fisheries industry. The concentration of chlorophyll a in the water is often used as an estimate for primary production, however, this measurement can only tell us the ‘end product’ from a long and complicated process, where a large part of the plant material is recycled. It is, therefore, more accurate and informative to measure the primary production rate in the process of estimating the amount of organic material and oxygen produced. In this study we analysed 1182 coastal water primary production measurements from the time period from 1998 to 2009. We expected primary production to be greatest during the spring bloom period. However, we found a general seasonal variation with the highest production during summer months. Production at this time was highly supported by a deeper primary production from below the pycnocline. This sub-pycnocline primary production accounts for app. 7–29 % of the annual primary production depending on the hydrodynamics in the area. For the specific study area (Baltic Sea transition zone), it accounts for almost half of the oxygen consumption in the waters below the pycnocline. This study shows that when including the sub-pycnocline primary production, not only the annual estimate increases, but also the seasonal variation changes. We therefore strongly suggest that no survey programs are based only on surface primary production measurements.