Following restoration changes in Antoninek Reservoir physico-chemical and biological processes in the water column and bottom sediments were measured to outline mechanisms of changes in nitrogen, phosphorus and organic matter concentrations during water flow through this reservoir. Intensive mineralisation of organic matter in the shallow sediments stimulated primary production and influenced increasing ammonia and nitrite nitrogen concentrations. Two main factors affected concentrations of phosphorus: (1) its presence in the external loads of river waters entering the reservoir, more important in the colder seasons as the water discharge was higher and (2) from the internal loads coming from bottom sediments. The quality of the river water during its flow through this reservoir improved for most parameters and seasons. However, concentrations of nutrients were still high in waters flowing out from the reservoir and in some months they were higher in the outflow than in waters entering the reservoir.