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Sediment trap material collected at five depths from two locations in Lake Michigan has been studied to determine the sources of particulate organic matter and the early diagenetic changes which occur during sinking of particles. Aquatic material dominates in shallower depths whereas land-derived material is more important in near-bottom depths. Organic carbon concentrations decrease with depth as a result of remineralization of organic matter by microbial activity and dilution by resuspended bottom sediments. Preferential remineralization of algal organic matter and downslope transport of particulate matter from coastal areas create differences in the lipid biomarker characteristics of settling particles found at different depths in the water column. Calculations of apparent decomposition rate constants from lipid distributions at different depths show that shorter chainlength n-alkanoic acids are degraded faster than longer components. Carbon and nitrogen isotopic compositions of total organic matter are nearly unaffected by large-scale amounts of remineralization during sinking.

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Dissolved organic carbon (DOC) in water sorbs or binds organic xenobiotics, reducing the amount of compound that is "freely dissolved" and therefore the amount bioavailable to Pontoporeiu hoyi. The apparent biological uptake rate constant for each compound is proportional to the inverse of the Aldrich humic acid concentration as a source of DOC. The log of the DOC concentration required to reduce the apparent uptake rate constant by 50% correlates well with the log of the partition coefficient to DOC determined by reverse-phase methodology for partition coefficients as low as lo4. Further, the partitioning to DOC determined by reverse-phase methodology and from the toxicokinetics in P. hoyi yields partition coefficients similar to those of Aldrich humics measured as DOC and DOC from Lake Michigan interstitial waters. The partition coefficients determined by the two methods correlate well and only vary by a constant bias of a factor of approximately 3. Thus the partition coefficient determined by reverse-phase methodology can be used to predict the bioavailable concentration of organic compounds in water containing DOC for P. hoyi.

Dissolved organic matter (DOM) in aquatic systems is known to reduce the bioavailability of heavy metals. Recent studies have shown similar reductions in bioavailability of organic contaminants. The mechanism for reduction, with Aldrich humics, was to reduce the freely dissolved, bioavailable, xenobiotic concentration by partitioning to DOM. This mechanism was also found to apply to organic contaminants in the presence of DOM from interstitial waters. A reversephase separation technique was used to measure the sorbed xenobiotic, and by difference from the total, the freely dissolved concentration of a contaminant permitting the calculation of a partition coefficient ( Krp) . Equilibrium partitioning of selected polycyclic aromatic hydrocarbon and polychlorinated biphenyl congeners to the DOM, in interstitial waters from several geographical sources, ranged over several orders of magnitude for a single compound. The reduction in bioavailability was measured by reduction in the conditional uptake rate constant for organic xenobiotics in the presence of DOM, for the amphipod Pontoporeiu hoyi (the major benthic invertebrate in the Great Lakes). Reduction in the conditional uptake rate constant versus controls was used to calculate a biologically determined partition coefficient ( K b ) . The log Krp was well correlated with log Kb, log Kb = 1.54(0.15) + 0.723(0.03) log Krp ( r 2 = 0.74, n = 195) over a range of three orders of magnitude in measured partition coefficient for individual compounds using DOM from different sources.

Benthic surveys were conducted in the southern basin of Lake Michigan and throughout the lake to assess trends in benthic populations, emphasizing recent changes in densities of the benthic amphipod Diporeia spp. and dreissenid mussels. In the southern basin, Diporeia populations declined 89%, 91%, and 45% between 1993 and 2002 at sites <30, 31–50, and 51–90 m, respectively. Lakewide, the population declined 65% between 1994–1995 and 2000. Over the same time period, dreissenid densities, particularly Dreissena bugensis, increased. Intensive studies at 45 m sites in the southeastern region examined changes in lipid content, age structure, and benthic food inputs relative to the hypothesis that food limitation was a factor in Diporeia's disappearance. As Diporeia densities declined to zero, length–weight remained unchanged, and lipid content generally increased. Recruitment still occurred, but the young did not survive to become adults. Based on organic carbon, biogenic silica, and chlorophyll collected in sediment traps and found in the upper sediments, pelagic inputs to the benthic region still occurred. Our field observations and laboratory experiments did not disprove the hypothesis that food limitation from dreissenid filtering activities was the cause of the decline, but direct relationships between the loss of Diporeia and indicators of food availability were difficult to establish.