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This study evaluated water quality, nitrogen (N), and phytoplankton assemblage linkages along the western Long Island Sound (USA) shoreline (Nov. 2020 – Dec. 2021) following COVID-19 stay-in-place (SIP) orders through monthly surveys and N-addition bioassays. Ammonia-N (AmN; NH3+NH4+) negatively correlated with total chlorophyll-a (chl-a) at all sites; this was significant at Alley Creek, adjacent to urban wastewater inputs, and at Calf Pasture, by the Norwalk River (Spearman rank correlation, p<0.01 and 0.02). Diatoms were abundant throughout the study, though dinoflagellates (Heterocapsa, Prorocentrum), euglenoids/cryptophytes, and both nano- and picoplankton biomass increased during summer. In field and experimental assessments, high nitrite+nitrate (N+N) and low AmN increased diatom abundances while AmN was positively linked to cryptophyte concentrations. Likely N+N decreases with presumably minimal changes in AmN and organic N during COVID-19 SIP resulted in phytoplankton assemblage shifts (decreased diatoms, increased euglenoids/cryptophytes), highlighting the ecological impacts of N-form delivered by wastewater to urban estuaries.