Levels of neurotoxic methylmercury (MeHg) in phytoplankton are strongly associated with water MeHg concentrations. Because uptake by phytoplankton is the first and largest step of bioaccumulation in aquatic food webs many studies have investigated factors driving seasonal changes in water MeHg concentrations. Organic matter (OM) is widely accepted as an important driver of MeHg production and uptake by phytoplankton but is also known for strong interannual variability in concentration and composition within systems. In this study, we explore the role of OM on spatial and interannual variability of MeHg in a subarctic coastal sea, the northern Baltic Sea. Using MeHg (2014: 80 +/- 25 fM; 2015: <LOD; 2016: 21 +/- 9 fM) and OM measurements during late summer/early fall, we find that dissolved organic carbon (DOC) and humic matter content explain 60% of MeHg variability. We find that while labile DOC increases MeHg levels in the water, humic content reduces it. We propose that the positive association between MeHg and labile DOC shows that labile DOC is a proxy for OM remineralization rate in nearshore and offshore waters. This is consistent with other studies finding that in situ MeHg production in the water column occurs during OM remineralization. The negative association between water humic content and MeHg concentration is most likely due to humic matter decreasing inorganic mercury (Hg-II) bioavailability to methylating microbes. With these relationships, we develop a statistical model and use it to calculate MeHg concentrations in late summer nearshore and offshore waters between 2006 and 2016 using measured values for water DOC and humic matter content. We find that MeHg concentrations can vary by up to an order of magnitude between years, highlighting the importance of considering interannual variability in water column MeHg concentrations when interpreting both short and long term MeHg trends in biota.