A combination of bathymetric surveying and bottom-sediment coring was used to investigate sediment deposition and the occurrence of selected nutrients (total nitrogen and total phosphorus), organic and total carbon, 26 metals and trace elements, 15 organochlorine compounds, 1 radionuclide, and diatoms in bottom sediment of Perry Lake, northeast Kansas. The total estimated volume and mass of bottom sediment deposited from 1969 through 2001 in the original conservation-pool area of the lake was 2,470 million cubic feet (56,700 acre-feet) and 97,200 million pounds (44,100 million kilograms), respectively. The estimated sediment volume occupied about 23 percent of the original conservation-pool, water-storage capacity of the lake. Mean annual net sediment deposition since 1969 was estimated to be 3,040 million pounds (1,379 million kilograms). Mean annual sediment yield from the Perry Lake Basin was estimated to be 2,740,000 pounds per square mile (4,798 kilograms per hectare).

The estimated mean annual net loads of total nitrogen and total phosphorus deposited in the bottom sediment of Perry Lake were 7,610,000 pounds per year (3,450,000 kilograms per year) and 3,350,000 pounds per year (1,520,000 kilograms per year), respectively. The estimated mean annual yields of total nitrogen and total phosphorus from the Perry Lake Basin were 6,850 pounds per square mile per year (12.0 kilograms per hectare per year) and 3,020 pounds per square mile per year (5.29 kilograms per hectare per year), respectively. A statistically significant positive trend for total nitrogen deposition in the bottom sediment of Perry Lake was indicated. However, the trend may be due solely to analytical variance. No statistically significant trend for total phosphorus deposition was indicated. Overall, the transport and deposition of these constituents have been relatively uniform throughout the history of Perry Lake.

On the basis of nonenforceable sediment-quality guidelines established by the U.S. Environmental Protection Agency, concentrations of arsenic, chromium, copper, and nickel in the bottom sediment of Perry Lake typically exceeded the threshold-effects levels, which represent the concentrations above which toxic biological effects occasionally occur. Most nickel concentrations also exceeded the probable-effects level, which represents the concentration above which toxic biological effects usually or frequently occur. Sediment concentrations of metals and trace elements were relatively uniform over time. Statistically significant positive depositional trends for arsenic and manganese and statistically significant negative depositional trends for beryllium, chromium, titanium, and vanadium were indicated. However, the trends may be due solely to analytical variance. Organochlorine compounds either were not detected or were detected at concentrations less than the threshold-effects levels. Evidence of a negative depositional trend for DDE (degradation product of DDT) was consistent with the history of DDT use. Other organochlorine compounds detected were DDD and dieldrin.

Diatom occurrence in the bottom sediment of Perry Lake was dominated by species that are indicators of eutrophic (nutrient-rich) conditions. Thus, it was concluded that eutrophic conditions have existed during much of the history of Perry Lake. However, an increase in the relative percentage abundance of the oligotrophic (nutrient-poor) species, combined with the significant positive depositional trends for two oligotrophic species (Aulacoseira islandica and Cyclotella radiosa) and the significant negative depositional trend for one eutrophic species (Stephanodiscus niagarae), indicated that conditions in Perry Lake may have become less eutrophic in recent years.

Notable changes in human activity within the basin included a substantial decrease in alfalfa production and a substantial increase in soybean production from 1965 to 2000. These and other changes in human activity may have had some effect on the deposition of chemical constituents and diatoms in the bottom sediment of Perry Lake. It is uncertain whether changes in human activity may account, in part, for the possibility of Perry Lake becoming less eutrophic over time as indicated by trends in the deposition of several diatom species in the lake-bed sediment.