Green sturgeon (Acipenser medirostris) is a highly migratory, marine oriented species that congregates in non-natal estuaries during summer and early fall. Individuals from the threatened Southern Distinct Population Segment (SDPS) and non-listed Northern Distinct Population Segment (NDPS) regularly co-occur in non-natal estuaries including the Columbia River estuary, Willapa Bay, and Grays Harbor in relative proportions not explained by abundance or distance from natal river. We used genetic markers to assign green sturgeon sampled in these estuaries from 2010 to 2012 to distinct population segments (DPS). We then examined interannual differences in DPS composition among estuaries. Fork length distributions were compared between SDPS and NDPS green sturgeon to determine whether size varied within and among DPSs and estuaries. The majority of green sturgeon sampled in the Columbia River estuary and Willapa Bay were assigned to the SDPS, while we assigned nearly even DPS proportions to our Grays Harbor samples. NDPS green sturgeon were significantly smaller than those originating from the SDPS within and among estuaries. We used these findings to develop several hypotheses about the mechanisms that may lead to specific patterns of non-natal estuary use. Genetic markers also assigned a single age-0 green sturgeon sampled in the Columbia River to the NDPS, although our analyses suggest that this individual’s parents may not have originated from known NDPS spawning populations. Because the Columbia River may serve as alternative spawning habitat for green sturgeon as climate change occurs, we recommend monitoring the Columbia River more closely for further evidence of green sturgeon spawning.