Sedimentary cores are widely used for studying Quaternary records. However, the amount of sediment that is available is proportional to the diameter of the core, which is rarely bigger than 15 cm. One way to obtain more sediment is to use two cores retrieved from almost the same location and use them as if they represent a unique sedimentary record. In the present work, an experimental design has been applied to verify if “twin cores” from an estuary can be considered as representing the same sedimentary record with twice the amount of sediment to study. Because sediment can be characterized based on its color, the variables used as replicates in the experimental design are the three Lab CIE colors acquired with a X-Rite Colortron spectrophotometer. Sediment cores were retrieved from the upper saltmarsh of Gilão River’s estuary, southern Portugal. Twin cores, with in between distances of 50 cm, 100 cm and 200 cm, from two different sites were analysed. Results from a nested ANOVA show that even for the closest twin cores (50 cm apart) there is at least one color variable that shows significant variations between the profiles of both cores. These results clearly show that “twin cores” cannot be used as a unique sedimentary record without any previous testing, at least in such transitional regions.