Despite various water protection measures, good water quality and reduction of nutrient loads seem very distant goals, largely due to limited knowledge of processes occurring in river valleys. Our study aimed at establishing the role of small floodplain reservoirs in the eutrophication processes, in the face of recent climate changes. The content of phosphorus and nitrogen compounds was determined in sediments and water of small floodplain reservoirs, (the Vistula River Valley, Poland) using spectrophotometric and Kjeldahl’s method. Nutrient loads in sediments were linked to the texture and total organic carbon content. Seasonal changes in water quality were strictly connected to changing weather conditions, flood and drought. The concentrations of PO43− and NO3− were found to rise after summer flooding. Increases in NH4+, total phosphorus (TP) and total nitrogen (TN) were correlated with the surface water area reduction in the reservoirs, which during the year of the study was on average 62%. Therefore, small floodplain reservoirs could be considered simultaneously as sinks and sources of nutrients. On the one hand, they accumulate P and N compounds carried by the river during the flood. On the other hand, climate change cause that small floodplain reservoirs may be responsible for enhanced biomass production.