Harmful algal blooms contribute to the dynamics of salt marsh ponds in a bar‐built estuary

Salt marsh ponds (SMPs) are a vital component of coastal wetlands, however, studies on microalgae and harmful algal blooms (HABs) in these systems remain limited. To address this gap, we investigated microalgal assemblages and the occurrence of HABs in SMPs on the Sheepshead Meadows Peninsula, New Jersey, across three marsh types: open marsh water managed, ditched, and unaltered. Monthly samples were collected from six SMPs between May 2022 and June 2023. Microalgae composition exhibited dynamic temporal changes in each pond and significant spatial heterogeneity across the ponds. This study is the first to document the widespread presence of HABs in SMPs under different marsh management regimes in this region. Identified HAB taxa included dinoflagellates Akashiwo sanguinea, Amphidinium carterae, Prorocentrum lima and Gymnodinium aureolum, raphidophytes Chattonella subsalsa and Heterosigma akashiwo, haptophyte Prymnesium parvum, and cyanobacteria Planktothrix agardhii, Lyngbya aestuarii. HAB species contributed > 60 % ∼ 98 % of total algal abundance in many cases, with cell densities reaching 10³ to 10⁴ cell/mL for dinoflagellates and up to 10⁵ cells/mL for P. parvum. Environmental variables such as water temperature, salinity, pH, and dissolved oxygen accounted for about 7 % of the algal community variance, suggesting other unmeasured factors influence HAB distribution. Our results indicate that the enclosed and semi-enclosed ponds may create favorable microhabitats for HAB proliferation. Additionally, the frequent undulations of the ponds may facilitate the transport of HAB species, making SMPs potential reservoirs for HABs in New Jersey’s wetlands and coastal waters. This study highlights the need to incorporate SMPs into long-term monitoring efforts to better assess salt marsh habitat conditions and ecological health risks associated with HABs.