Resumo. Abstract Aim: Current study assessed the influence of hydrometric levels on the limnological characteristics of two river floodplain systems in the Ribeira do Iguape Basin (state of São Paulo, Brazil). Methods: Rainfall data were collected dailyfrom an automatic weather station in Jacupiranga SP Brazil and daily hydrometric level records were obtained from automatic linigraphs installed on the two adjacent rivers. Moreover, pH, electrical conductivity and dissolved oxygen were measured by a multiparametric probe. Water samples were collected to analyze nitrate, ammoniac nitrogen, total nitrogen and phosphorus, total alkalinity and suspended material. The samplings were carried out in April and July, representative months for low and high water periods, respectively. Results and Conclusions: Statistical analysis highlighted the “effect of homogenization”, attributed to the hydrological pulses in several studies carried out in river-floodplain systems. This effect in current study was more underscored at Lagoon 2, which remained connected for a longer period with the adjacent river, when compared to Lagoon 1- River Jacupiranguinha system. Higher dissolved oxygen concentrations at Lagoon 2, in contrast with the Lagoon 1 featuring anoxia during the whole period under analysis, were also attributed to the above-mentioned greater hydrological connectivity. Current study highlights that the water-mediated transferences during the high water period may contribute not only towards the fertilization of marginal lagoons (inputs of nutrients and organic matter) but also to significant pollutant loads, according to land use along the watersheds. In the case of Lagoon 1- River Jacupiranguinha system, even though further studies are needed and strongly recommended, it is reasonable to assume that the discharges of mining effluents into the river may result in ecological damage not only to the receiving water body but also to the connected ecosystems.