The main objective of this study was to evaluate the functional traits regarding bioturbation activity and its influence in the nutrient cycling of the native clam species Ruditapes decussatus and the invasive species Ruditapes philippinarum in Ria de Aveiro lagoon. Presently, these species live in sympatry and the impact of the invasive species was evaluated under controlled microcosmos setting, through combined/manipulated ratios of both species, including monospecific scenarios and a control without bivalves. Bioturbation intensity was measured by maximum, median and mean mix depth of particle redistribution, as well as by Surface Boundary Roughness (SBR), using time-lapse fluorescent sediment profile imaging (f-SPI) analysis, through the use of luminophores. Water nutrient concentrations (NH4-N, NOx-N and PO4-P) were also evaluated. This study showed that there were no significant differences in the maximum, median and mean mix depth of particle redistribution, SBR and water nutrient concentrations between the different ratios of clam species tested. Significant differences were only recorded between the control treatment (no bivalves) and those with bivalves. Thus, according to the present work, in a scenario of potential replacement of the native species by the invasive species, no significant differences are anticipated in short- and long-term regarding the tested functional traits.