Cold seeps are seafloor manifestations of fluid flow from deeper within marine sediments, and they are often locations where methane discharges into the ocean. These dynamic environments are typically found along continental margins and serve as biological oases for specialized seafloor macro- and meio-fauna as well as seafloor and subseafloor chemoautotrophic microorganisms. Microbial methanogenesis is ubiquitous in the upper few 100s of meters of sediments along continental margins and, as such, continental margin sediments constitute an enormous geologic reservoir of methane. Methane exists as a dissolved component of pore water within continental margin sediments and concentrations are often high enough that methane can also exist as a free gas or is stored in methane hydrates. Burial of dissolved methane in pore water and sequestration within methane hydrate represent two important sinks that prevent the release of this greenhouse gas into the ocean/atmosphere system. The largest sink of microbial methane within marine sediments is the anaerobic oxidation of methane (AOM) performed by a syntrophic consortium of bacteria and archaea within pore water. Bisulfide produced by this reaction is transported to the seafloor where it serves as a key metabolic component for thiotrophic organisms. The amount of methane oxidized through AOM is variable but can be up to 100% of the dissolved methane flux to the seafloor. The reasons for variability in the efficiency of this process remains a pivotal unknown impacting estimates of methane input to the ocean from marine sediments. This dissertation explores the response of cold seep and methane hydrate systems to environmental variability. Chapter 1 presents an introduction to microbially-mediated reactions in marine sediments including microbial methanogenesis and the anaerobic oxidation of methane, the global methane hydrate reservoir, and the importance and characteristics of the organisms involved in the vital process of AOM. In Chapter 2, pore water geochemical tracers are used to test the hypothesis that contemporary bottom water warming along the Washington sector of the Cascadia margin has induced widespread dissociation of buried methane hydrate along the upper continental slope where the reservoir is most sensitive to changes in bottom water temperature. This work reveals that fluid emitted at actively venting seeps in this region is largely sourced from deeper mineral dehydration reactions and from meteoric water discharge, and is not the result of modern methane hydrate dissociation. Chapter 3 presents the longest continuous record of time-series fluid flow rate and composition data at a cold seep to date. The time-series record documents the persistent downward flow of seawater directly beneath a Beggiatoa bacterial mat. Beggiaotoa is a filamentous bacterium common in reducing environments such as cold seeps that requires the upward flux of reduced sulfur for survival. Geochemical modeling shows that downward flow of fluid rich in electron acceptors stimulates enhanced rates of sulfate reduction and bisulfide production via AOM, driving a strong diffusional gradient of bisulfide to the seafloor. These results show that Beggiatoa can persist and thrive in regions of downward fluid advection, and that the shallow circulation of seawater at cold seeps increases the consumption of oxygen, nitrate, and sulfate from seawater, influencing local biogeochemical cycling The research presented in Chapter 4 explores the possibility that anaerobic methanotrophic (ANME) archaeal communities involved in AOM are limited by the bioavailability of nickel in cold seep pore water, thus potentially impacting the efficiency of AOM in oxidizing methane before it can escape to the water column. Data presented in this chapter show that higher concentrations of bioavailable nickel exist at non-cold seep settings compared to cold seep settings where there is likely greater uptake and utilization of nickel from pore water to fuel ANME communities. It may be that ANME have successfully developed an evolutionary adaptation to acquire nickel from non-bioavailable forms, such as the production of nickel-specific extracellular ligands similar to siderophores. One or more of the organic ligands characterized in this study may be the result of such ligand expression. This study is the first to measure the bioavailability of nickel in marine pore water as well as to quantify and characterize organic nickel-binding ligands.