Despite a recent proliferation of bridges in coastal zones, little is known of the long-term impacts of bridge construction on phytoplankton abundance and community composition in nearshore waters. Here, we used high performance liquid chromatographic (HPLC) analysis to quantify historical changes in phytoplankton using fossils from cores on either side of a 57-year-old bridge that reduced fetch by 76\% and created a discrete enclosed inner embayment. We hypothesized that phytoplankton abundance should be greater in the inner bay after bridge construction due to reduced hydrological flow and increased nutrient influx associated with terrestrial development and more profound anoxia in the enclosed basin. As expected, primary producer abundance, especially cryptophytes, increased in the inner bay during the 1950–1960s, although the effect was transient despite continuous fourfold elevation in sediment organic matter content (\%C, \%N) after ca. 1960 in response to wastewater influx. The pulse in cryptophytes appeared to correspond to influx of humic-rich waters derived from locally exploited peatlands, whereas the phytoplankton community of the outer basin largely reflected historical variations in climate, with warmer April months associated with increased abundance of diatoms and cryptophytes. Overall, sediment stable isotope values in the inner basin varied in response to a complex combination of changes in wastewater treatment (δ 15 N), release of untreated fish plant effluents (δ 15 N), and connectivity with the open ocean (δ 13 C). Taken together, these findings suggest that the effects of bridge construction on coastal phytoplankton production and community composition operated through multiple pathways, rather than just via modifications of basin hydrology. © 2018, Coastal and Estuarine Research Federation.