Macrophytes play key functional and structural roles in floodplain shallow lakes (SL), determining the maintenance of ecosystem functions and sustaining several productive activities. We assessed the relationship between macrophyte community structure (composition, species abundance, and plant diversity) and environmental features (SL dynamics, connectivity, morphometry, flood frequency, and water and sediment physical and chemical variables) in the Lower Paraná River floodplain. Our main hypothesis was that SL macrophyte distribution depends on direct and indirect environmental controls operating at multiple scales. The SL dynamics during the April–November 2017 Paraná River pulse were described according to their coverage changes (vegetation, and turbid or clear open water), which were assessed with supervised classifications on Landsat 8-OLI scenes. Twenty-five SL of the Lower Paraná River floodplain were selected to represent all the SL dynamics identified. Ten SL were permanently connected and 15 were disconnected from watercourses. Water and sediment physical and chemical characteristics, macrophyte assemblage composition, and plant species abundance were surveyed at each site in the 2018 summer. Also, SL morphometric parameters and flood frequency were estimated from ancillary geographic data. The direct controlling factors of macrophyte assemblages were water ammonium and water nitrate concentrations, turbidity, and flood frequency. No clear effects of environmental conditions on macrophyte diversity were found. The connectivity of SL with watercourses affected their water and sediment physical and chemical features. Also, SL dynamics during the 2017 pulse were related to flood frequency. As connectivity to watercourses affects SL chemical and physical variables, and SL dynamics were associated with flood frequency, connectivity and SL dynamics indirectly influenced macrophyte assemblage composition. This study improved our understanding of macrophyte distribution patterns in the study area, which was related to several environmental variables operating at different scales. Our results highlight the importance of the variability of hydrological connectivity in promoting environmental heterogeneity in river floodplain systems, which is central to their functioning, and the high biodiversity that characterises these environments.