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Monitored Natural Attenuation (MNA) has emerged as a well recognized approach for the remediation of BTEX contaminated aquifers. In order to deem MNA as an adequate remediation scheme, their must exist proof of the occurrence of biodegradation processes at the site of interest. Furthermore, a comprehensive understanding of the coupled physical (e.g., advective transport, diffusion, and sorption) and biological (microbially-catalyzed contaminant degradation) processes, acting on the compound(s) of interest, is required to judge the natural attenuation potential of a certain site. This thesis is organized in two main parts. The first part focuses on the effects of transverse dispersion and sorption on the stable-carbon isotope signature of organic contaminants, and its potential interference with the assessment of in-situ biodegradation by compound-specific isotope analysis (CSIA). I performed scenario simulations for fringe-controlled ethylbenzene degradation in steady-state contaminant plumes, and analyzed a toluene-pulse experiment performed in an indoor model aquifer via reactivetransport modeling. The results of these two studies indicate that physical processes may affect the isotope signature of organic contaminants in groundwater systems, by either acting as rate-limiting step for biodegradation (e.g., transverse mixing in fringecontrolled biodegradation) or fractionating themselves between isotopically light and heavy contaminant molecules (e.g., transverse dispersion and sorption). The second part of this thesis addresses the influence of transient environmental conditions, such as the temporal absence of electron donors and/or acceptors (which might arise, e.g., due to changing hydraulic conditions) on in-situ biodegradation. I analyzed toluene degradation experiments, performed under aerobic conditions in one and two-dimensional bench-scale porous flow-through systems, by reactive-transport modeling. The analysis indicated that temporal periods of starvation of up to four months, which were induced in the experiments by interrupting the injection of the growth-substrate toluene, did not drastically reduce the biodegradation potential. To capture the dynamics of the system, the numerical modeling approach necessitated the inclusion of microbial dormancy, i.e., the switch to an ’inactive’ state of low metabolic activity under unfavorable conditions, as well as peak cell detachment during growth of sessile bacteria.