|dc.description.abstract||Light dependent and independent reactions produce and consume reactive oxygen species (ROS), including hydrogen peroxide (H2O2) and superoxide (O2-), in natural waters. ROS can act as oxidants or reductants to biologically important metals such as Fe, Cu, and Mn influencing their bioavailability. ROS produced in natural waters have also been linked to global phenomena such as harmful algal bloom fish kills and coral bleaching. In this thesis, we focus on the light independent (dark) reactions of ROS that are produced and decomposed by particle-associated processes, most likely microorganisms. However, before microorganisms can be implicated in ROS reactions we need to understand where, why, and how microorganisms as well as abiotic processes produce and decompose ROS. Ecological and geochemical stress factors that trigger ROS production and decomposition in natural waters are largely unknown. Therefore, we set out to measure the temporal and spatial variability of dark H2O2 production rates (PH2O2) and dark decay rate coefficients (kloss,H2O2) in freshwaters with a range of trophic states. Production rates were found to be comparable to production by photochemical processes. Furthermore, kloss,H2O2 correlated well with biological indicators (chlorophyll and cell counts) while PH2O2 did not. This suggests that while microorganisms are a common sink of H2O2, dark production may vary with microbial composition. We suspect that both a lake’s trophic state and the specific microbial consortia present in the system, at a given time, lead to the observed variability of ROS production in freshwater. The method for measuring dark PH2O2 in project one, which utilized an isotope tracer (H218O2), proved tedious, costly, and time consuming. Therefore, we used Amplex Red (AR) oxidation by H2O2 in the presence of horseradish peroxidase (HRP) catalyst as an effective alternative. We show that AR/HRP is suitable for measuring dark PH2O2 in freshwater by examining possible false positive and negative interferences, and methods to eliminate them. Catalase and HRP-free controls helped validate the AR method and revealed dark PH2O2 values of comparable magnitude and natural variability as previous studies. The dark redox cycling of mercury (Hg), especially the production of Hg(II), can lead to the formation of toxic methylated Hg compounds. Because dark reactions of Hg are largely an enigma and ROS are known to affect the redox cycling of metals in the ocean (e.g. Cu and Mn), we set out to understand if O2- plays a role in the dark biogeochemical cycle of Hg. Here, we measured O2- oxidation and reduction of Hg in filtered coastal (Vineyard Sound) seawater. O2- appeared to indirectly oxidize Hg0 in two seawater samples and O2- reduced Hg(II) in one seawater sample. We did not observe evidence of oxidation or reduction of Hg via secondary O2- reactions involving Mn, Cu, and nicotinamide adenine dinucleotide (NADH). However, our samples were filtered, and the proximity of NADH to cell surfaces may reveal a potential biological mechanism of Hg(II) reduction. The calculated reduction rate constant of Hg(II), 6.9 (3.1) x102 M-1 s-1, would cause a Hg(II) reduction rate of ~1% day-1 similar to the rate observed in previous studies of dark microbial Hg(II) reduction. Our study suggests that O2- may play an important role in the dark biogeochemical cycling of Hg in coastal ocean waters by indirectly oxidizing Hg0 and slowly reducing Hg(II).