Forests play a significant role in the mitigation of climate change through carbon storage and sequestration. However, a forest’s capacity to absorb carbon is influenced by a number of factors, such as soil characteristics, the selection of tree species, and the application of silvicultural practices. A study in Latvia was conducted to evaluate the carbon stock and sequestration potential of birch, common aspen, black alder and grey alder growing on periodically waterlogged and drained organic soils. Empirical data of forest resources were obtained from the National Forest Inventory (NFI) from 2016 to 2020. The findings indicate that black alder may thrive in both soil types, as it showed the best increase in carbon stock in periodically waterlogged soils, reaching a maximum of 129 t C haE−1 at the age of 61–70 years. Greater carbon sequestration in tree biomass occurs on drained soils compared to periodically waterlogged. Birch, aspen, and black alder stands may store between 106 and 119 t C haE−1 at age of 61 and 70 years, which is similar to grey alder stands at ages of 31–40 (114 ± 0.73 t C haE−1). Therefore, a short rotation for grey alder growing on drained organic soils could maximize carbon accumulation and add substitution value. These results suggest that different types of deciduous trees have varying capacities for carbon storage and sequestration, and that it’s important to consider site-specific factors, rotation age and silvicultural practices when aiming to maximize carbon sequestration in tree biomass.