Lake Pepin is a large, natural riverine lake in the upper Mississippi River downstream of the Twin Cities metropolitan area and the confluence with the Minnesota River, which are sources of suspended sediments and pollutants (nutrients and potentially toxic materials). The lake has a history of water quality problems and has been an efficient trap for suspended sediment and sediment-associated contaminants. Based on bathymetric survey data, the loss of volume in Lake Pepin between 1897 and 1986 was estimated. The mass balance of the lake for total suspended solids, chlorophyll a, total and dissolved reactive phosphorus and total nitrogen for 9 June 1987 to 4 June 1988 was also estimated. Water was sampled at the inflow, mid-reach, and outflow of the lake. Lake Pepin is very eutrophic, based on concentrations of phosphorus, nitrogen and chlorophyll a. The lake volume decreased by approximately 21% between 1897 and 1986. Longitudinally, the greatest fraction of the whole-lake volume loss occurred in the upper lake (45%). Based on mass balance calculations, the lake trapped about half of the suspended solids entering the lake, but it had a small net export of chlorophyll a. The lake was a sink for phosphorus and nitrogen; however, it had a net export of total phosphorus at times during low flows in the summer of 1987. Internal loading of dissolved reactive phosphorus was prevalent during the summer of 1987. The only substantial export of total nitrogen occurred in June 1987 during a bloom of cyanobacteria. The lake should continue to be an efficient trap for suspended sediment and associated contaminants, but its trapping efficiency will continue to decline slowly as lake volume decreases. Lake Pepin will probably continue to experience water quality problems, such as nuisance algal growths and low dissolved oxygen, especially during summer low flows.