Fossil plant assemblages are described in their sequence stratigraphic context from the Upper Carboniferous (Langsettian) Joggins Formation of Nova Scotia to elucidate ecosystem response to transgressive–regressive rhythms. Results show that rising base level resulted in retrograding submerged coastal mires co-dominated by Lepidodendron and Lepidophloios, which were replaced by short-lived Paralycopodites communities immediately following mire drowning. Extensive brackish bays existed during early highstand, distally fringed by gymnospermous and putative progymnospermous coastal and/or upland vegetation. Late highstand bay filling generated prograding distributary wetlands dominated by flood-disturbed lycopsid–pteridosperm–sphenopsid communities, and locally by cordaite mangroves. As base level fell, well-drained alluvial plains were dominated by fire-prone cordaite and/or Sigillaria communities, which persisted until the next phase of base-level rise. This rhythmic ecosystem succession repeatedly occurred on a c. 50–200 ka time scale, and was probably driven by glacial–interglacial climate rhythms.