The turnover of phosphorus and nitrogen have been studied in a low salinity estuary in the Bothnian Sea. The estuary, Gardsfjarden, has a high loading of nutrients from a pulp and paper mill which supplies the estuary with three times the annual natural input of phosphorus and nitrogen, respectively. The turnover of nutrients was to a great extent determined by hydrodynamic variations. During periods of intense resuspension there was a net export of particulate bound nutrients from the estuary to the sea but since these periods were short there was an overall net retention of particulate nutrients. The estuary was a source for dissolved phosphorus to the sea. The major source of phosphorus export was release of dissolved P from anoxic sediments. Gardsfjarden was a sink for dissolved nitrogen which most likely escaped the estuary by denitrification. Nitrate was supplied by degradation of particulate organic nitrogen but the main source was import from the sea.