Mangrove forests provide important ecosystem services to the human society and nature including mitigation of climate change. The quality and quantity of ecosystem services offered by mangrove forests are however at risk when mangroves are degraded. The restoration of mangrove areas is considered as a natural solution to recover lost ecosystem services such as securing of carbon stocks. This study was set to assess the extent to which mangrove planting activities compensate for the loss of biomass carbon stocks and other structural attributes in Rufiji Delta-Tanzania through analysis of biomass carbon loss and gain as a result of conversion of mangroves forest into rice farms and planting of mangroves respectively. Circular sampling plots were established in good, degraded and restored mangrove areas where total tree heights and Diameter at Breast Height (DBH) of all standing trees were measured and recorded by species and used to compute biomass carbon stock. The mangrove species composition changed from 7 in 1989 to 2 species in degraded plots in 2016. The species dominance changed from Avicennia marina in 1989 to Rhizophora mucronata in 2016 in good mangrove plots and from A. marina and Sonneratia alba to an invasive Baringtonia racemosa in degraded plots. Bruguiera gymnorrhiza was the only mangrove species used for restoration through planting in the delta and the overall survival rate was 37%. The above-ground carbon (AGC) and below-ground carbon (BGC) for the good natural mangrove plots ranged from 28.18 to 299.43 and 16.00–164.51 Mg C ha−1 respectively compared to 0–150.88 and 0–967.01 Mg C ha−1 in the degraded plots. The total biomass carbon stock in the good natural mangrove plots ranged from 44.14 to 463.94 Mg C ha−1 while for the degraded plots the range was 0–247.89 Mg C ha−1. The carbon stocks in 5, 10 and 15 year old planted mangroves were 13.65, 20.13 and 57.53 Mg C ha−1 respectively. The biomass loss of 172.91 Mg C ha−1 was estimated in a period of 25 years (1989–2016), equivalent to an annual loss rate of 6.9 Mg C ha−1year−1, demonstrating that degradation has a significant contribution to loss of carbon stocks. Nevertheless, an average of 3.8 Mg C ha−1year−1 was stocked by 15 years old planted mangroves, demonstrating that there is potential for the planted mangroves to compensate for the lost carbon if the anthropogenic drivers such as rice farming is controlled. These findings call for urgent collective actions among stakeholders to consider and improve the integrated management of the delta.