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Primary producer responses to cumulative regulating factors were investigated in a temporarily closed microtidal estuary. We hypothesised that the phytoplankton chlorophyll- a  concentration (Chl  a ) and invasive alien aquatic plant (IAAP) abundance would be highest during the low-flow season and that shifts in community structure would be driven by salinity and nutrient gradients. The augmented freshwater inflow limited phytoplankton Chl  a  (&lt;5 µg Chl  a  l −1 ) due to low freshwater residency, while isolated instances of increased Chl  a  (≥10 but ≤20 µg Chl  a  l −1 ) were recorded following a brief period of mouth closure. Cyanophyceae proliferated for 67% of the study period with maximum abundance (&gt;10 000 cells ml −1 ) recorded in spring owing to increased water retention. A community consisting of co-dominant Cryptophyceae, Euglenophyceae and IAAPs was recorded during winter, indicating a shared preference for slow-flowing, low-salinity (&lt;5) eutrophic habitats. Dinophyceae was the only phytoplankton class that showed niche differentiation by favouring the mesohaline lower reaches. The homogenisation of dynamic estuarine gradients and the prevalence of nutrient-tolerant primary producers is indicative of the degraded state of this estuary as a result of consistent nutrient-enriched freshwater baseflows. The application of a multidisciplinary restoration approach is required to improve the ecosystem health.

Flow alterations and nutrient loading reduce primary producer variability in a temporarily closed microtidal estuary in KwaZulu-Natal, South Africa