The Bug River, in the section between Dorohusk and Włodawa (part of the eastern UE border), is one of the last remaining natural rivers in Europe. Thus, its abundance of floodplain lakes (FPL) in that part constitutes an area which preserves biodiversity. This study presents an analysis of potamophases duration and the Potamophases Concentration Index (PCI) in 20 floodplain lakes in the multi-year period 1952–2014. One-way analysis of variance (ANOVA, Tukey test), as well as a correlogram approach were used to perform statistical analyses. Among the lakes, few differed significantly from the others; more often, differences between years, in terms of both potamophase duration and PCI, were found. This proved that time is more important than space in shaping river valley hydrology. Cumulative values of the study indices, presented in a correlogram, showed that both potamophase duration and the period of potamophase concentration determine the water quality of a floodplain lake, expressed as the hydro-chemical type. In floodplain lakes with short potamophases concentrated at the beginning of a hydrologic year, water quality typical for interzonal lakes was observed; in floodplain lakes with the longest potamophases with their concentration at the end of a hydrologic year, ionic concentrations typical of extrazonal lakes occurred, whereas in lakes with a potamophase duration close to the average value and a spring concentration of floods, intermediate water quality was observed, typical of mixozonal lakes. A sound knowledge of floodplain lake functioning is crucial to maintaining the biodiversity of river valleys due to the lake's natural water and nutrient storage capacity.