RESEARCH ARTICLE Environmental factors controlling phytoplankton dynamics in a large floodplain river with emphasis on cyanobacteria Shawn M. Giblin 1 | Gretchen A. Gerrish 2 1 Wisconsin Department of Natural Resources, La Crosse, Wisconsin 2 River Studies Center and Biology Department, University of Wisconsin La Crosse, La Crosse, Wisconsin Correspondence Shawn M. Giblin, Wisconsin Department of Natural Resources, La Crosse, WI 54601. Email: shawn.giblin@wisconsin.gov Present address Gretchen A. Gerrish, University of Wisconsin Madison, Trout Lake Station and Center for Limnology, Boulder Junction, Wisconsin, WI 54512. Funding information U.S. Army Corps of Engineers' Upper Mississippi River Restoration Program, Long Term Resource Monitoring (LTRM) element Abstract Harmful algal blooms are occurring in large river ecosystems and at the mouth of large rivers with increasing frequency. In lentic systems, the chemical and physical conditions that promote harmful algal blooms are somewhat predictable but track- ing prevalence and conditions that promote harmful algal blooms in lotic systems is much more difficult. We captured two of the most extreme discharge years within the last 20 years occurring in the Upper Mississippi River, allowing a natural experiment that evaluated how major shifts in discharge drive environmental varia- tion and associated shifts in phytoplankton. Statistical models describing signifi- cant environmental covariates for phytoplankton assemblages and specific taxa were developed and used to identify management-relevant numeric breakpoints at which environmental variables may promote the growth of specific phytoplankton and/or cyanobacteria. Our analyses supported that potentially toxin-producing cyanobacteria dominate under high phosphorus concentration, low nitrogen con- centration, low nitrogen-to-phosphorus ratio, low turbulence, low flushing, ade- quate light and warm temperatures. Cyanobacteria dominated in 2009 when low discharge and low flushing likely led to optimal growth environments for Doli- chospermum, Aphanizomenon and Microcystis. Rarely will a single factor lead to the dominance, but multiple positive factors working in concert can lead to cyano- bacteria proliferation in large rivers. Certain isolated backwaters with high phos- phorus, low nitrogen, warm water temperatures and low potential for flushing could benefit from increased connection to channel inputs to reduce cyanobacterial dominance. Numerous examples of this type of habitat currently exist in the Upper Mississippi River and could benefit from reconnection to chan- nel habitats. KEYWORDS algal blooms, connectivity, cyanobacteria, eutrophication, phosphorus, phytoplankton, Upper Mississippi River 1 | INTRODUCTION Toxic cyanobacteria blooms are on the rise globally and are occurring in large river ecosystems and at the mouth of large rivers with increas- ing frequency (Huisman et al., 2018; O'Neil, Davis, Burford, & Gobler, 2012; Paerl & Otten, 2013). Algal blooms cause decreased clarity, reduced macrophytes, oxygen depletion, fish kills and the pro- duction of cyanotoxins (Paerl & Otten, 2013). The production of cyanotoxins can result in illness and/or death of exposed pets and occasionally humans. Cyanotoxins are especially concerning when Received: 4 December 2019 Revised: 22 May 2020 Accepted: 25 May 2020 DOI: 10.1002/rra.3658 River Res Applic. 2020;1–14. wileyonlinelibrary.com/journal/rra © 2020 John Wiley & Sons Ltd 1