Although microplastics (MP) have been documented in estuarine habitats, limited published data exist for New Hampshire and northern Massachusetts hampering meaningful, regional comparison with other geographies. Here we synthesize previously unpublished data from several independent baseline studies spanning three estuarine systems including Great Bay Estuary (GBE), Hampton-Seabrook Estuary (HSE), and Great Marsh Estuary (GME) to compare geographic data for MP to other published regional studies. Data include water column in GBE (n = 179 from 7 sites), surface waters and salt marsh sediment cores from HSE (n = 72 water samples from 12 sites and n = 77 sediment cores from 8 sites), and surface waters from GME (n = 42 water samples at 17 sites). Samples were analyzed for MP characteristics initially via either automated confocal microscopy or light microscopy, allowing initial estimation of the number and size distribution of putative MP. Particles from representative samples were analyzed using laser direct infrared spectrometry (LDIR) to determine elemental analysis. MP were found in > 98% of samples collected including surface waters, water column, and marine sediments. Counts ranged from 1 to 144,000 MP particles m-3 and mean MP differed significantly among regions, sites within regions, and across years. In the GBE water column, MP tended to peak during June-August in 4 of the 5 years studied. Most MP were roughly circular and ~50 μm in diameter. LDIR confirmed that many types of plastics are in these estuarine waters and also revealed that despite the digestion processes, biogenic materials often remained, predominantly chitin, rubber, wood, and coal. These data allow us to address the realistic levels of risk that estuarine MP pose in NH and northern MA estuaries and can be used to populate existing hydrodynamic models that will predict the tributary sources, movements, and fate of MP within these aquatic habitats.