The Pacific blue mussel (Mytilus trossulus) is a foundation species in high-latitude intertidal and estuarine systems that creates complex habitats, provides sediment stability, is food for top predators, and links the water column and the benthos. M. trossulus also makes an ideal model species to assess biological responses to environmental variability; specifically, its size frequency distributions can be influenced by the environment in which it lives. Mussels that inhabit estuaries in high latitudes receive freshwater runoff from snow and glacial-fed rivers or can be under oceanic influence. These hydrographic conditions work together with local static environmental characteristics, such as substrate type, fetch, beach slope, distance to freshwater, and glacial discharge to influence mussel demographics. In 2019 and 2020, mussels were collected from two Gulf of Alaska ecoregions to determine whether mussel size frequencies change over spatial (local and ecoregional) and hydrographic scales and whether any static environmental characteristics correlate with this variability. This study demonstrated that mussel size frequencies were most comparable at sites with similar hydrographic conditions, according to the ecoregion and year they were collected. Hydrographic conditions explained approximately 43% of the variation in mussel size frequencies for both years, for the combined ecoregions. Mussel recruits (0–2 mm) were more abundant at sites with higher fetch, while large mussels (> 20 mm) were more abundant at more protected sites. Fetch and freshwater influence explained most of the variation in mussel size frequencies for both years and across both ecoregions, while substrate and slope were also important in 2019 and glacial influence in 2020. This study suggests that hydrographic and static environmental conditions may play an important role in structuring mussel sizes. Although differences in mussel size frequencies were found depending on environmental conditions, mussel sizes showed little difference across differing types of freshwater influence, and so they may be resilient to changes associated with melting glaciers.