Efficient and sustainable management of rapidly mounting environmental issues has been the focus of current intensive research. The present study aimed to investigate the impact of plant phenological development stage variation on mercury (Hg) tolerance, accumulation, and allocation in two salt marsh macrophytes Triglochin maritima and Scirpus maritimus prevalent in historically Hg-contaminated Ria de Aveiro coastal lagoon (Portugal). Both plant samples and the sediments vegetated by monospecific stands of T. maritima and S. maritimus were collected from reference (R) and sites with moderate (M) and high (H) Hg contamination in Laranjo bay within Ria de Aveiro lagoon. Hg tolerance, uptake, and allocation in T. maritima and S. maritimus, physico-chemical traits (pH, redox potential, and organic matter content) and Hg concentrations in sediments vegetated by these species were impacted differentially by phenological development stages variation irrespective of the Hg contamination level. In T. maritima, Hg concentration increased with increase in Hg contamination gradient where root displayed significantly higher Hg followed by rhizome and leaf maximally at H. However, in S. maritimus, the highest Hg concentration was perceptible in rhizome followed by root maximally at M. Between the two studied plant species, S. maritimus displayed higher Hg tolerance index (depicted by higher plant dry mass allocated to reproductive stage) and higher available Hg at M (during all growth stages) and H (during senescent stage) when compared to T. maritimus. Both plant species proved to be Hg excluder (low root/rhizome-leaf Hg translocation). Additionally, T. maritima also acted as Hg stabilizer while, S. maritimus as Hg accumulator. It can be inferred from the study that (a) the plant phenological development stage variations significantly influenced plant Hg sensitivity by impacting sediment chemistry, plant growth (in terms of plant dry mass), Hg accumulation, and its subsequent allocation capacity, contingent to Hg contamination gradient; (b) S. maritimus accumulated higher Hg but restricted its translocation to above-ground part using exclusion process at both M and H due to its accelerated growth during Hg-tolerant reproductive/metabolically active phenological development stage greater than its counterpart T. maritima; and (c) the studied salt marsh plants although hailed from the same C3 and monocot group did not necessarily display similar phenotypic plasticity and behavior towards Hg-contaminated scenario during their life cycle.