It is frequently assumed that taking samples of soft marine sediments using surface-based gravity coring equipment causes minimal disruption to their sedimentological, biogeochemical, and biological condition. This assumption was evaluated by examining the potential disturbances caused when obtaining softsediment samples either by SCUBA or Craib-coring, comparing sediment oxygen microprofiles, benthic oxygen flux rates and sediment solid phase analyses (chlorophyll a (Chl a), organic carbon, and porosity) between both methods and against reference values measured in situ by benthic lander. The two sampling methodologies were tested in shallow coastal environments on the west coast of Scotland and generally the results obtained from cores collected using SCUBA exhibited values closest to those observed in situ. Oxygen penetration depth was significantly shallower in cores obtained by Craib-corer compared with the SCUBA cores. Craib cores also produced higher oxygen uptake rates which could be caused by greater levels of sediment disturbance during sampling. In addition, more homogenous levels of Chl a in the top 1 cm of the Craib cores, compared with the SCUBA samples, may indicate either resuspension or compression during gravity coring. Using SCUBA for shallow-water soft-sediment sampling permits steady and controlled coretube insertion and extraction, and more measured retrieval of the cores to the surface; this probably accounts for the observed differences. Whereas benthic lander-based in situ measurement would be the preferred method for analyzing sediment parameters in detail in this type of environment, SCUBA-based sampling offers a more accurate alternative to surface-based gravity coring.The ability to extract sediment samples that retain their in situ sedimentological, biogeochemical, and biological conditions is central to many marine and limnic investigations. The widespread demand for such observations has resulted in the application of a large array of different sediment sampling techniques (Blomqvist 1991). However, comparative assessments of these techniques and how well they represent in situ conditions are limited and focus mainly on the biological parameters measured in the samples (Blomqvist 1991). Glud et al. (1994Glud et al. ( , 1999 found shallower oxygen penetration depths (OPD), steeper oxygen concentration gradients and higher sediment oxygen uptake rates near the sediment surface in deep sea sediment cores incubated on board ship (ex situ) compared to the OPD and oxygen uptake rates recorded by an in situ benthic lander (Tengberg et al. 1995). Enhanced sediment nutrient concentrations have also been found in porewaters extracted ex situ (by core slicing and centrifugation) compared with data retrieved in situ using passive-equilibration "peepers" (Jahnke et al. 1989;Hammond et al. 1996;Aller et al. 1998). Hall et al. (2007 found sharp sub-surface maxima of the ratio of dissolved organic carbon (DOC) to dissolved organic nitrogen (DON) and carbohydrates in deep-sea retrieved sed...