Seagrass meadows store significant carbon stocks at a global scale, but land-use change and other anthropogenic activities can alter the natural process of organic carbon (C_org) accumulation. Here, we assessed the carbon accumulation history of two seagrass meadows in Zanzibar (Tanzania) that have experienced different degrees of disturbance. The meadow at Stone Town has been highly exposed to urban development during the 20th century, while the Mbweni meadow is located in an area with relatively low impacts but historical clearing of adjacent mangroves. The results showed that the two sites had similar sedimentary C_org accumulation rates (22–25 g m⁻² yr⁻¹) since the 1940s, while during the last two decades (∼1998 until 2018) they exhibited 24–30% higher accumulation of C_org, which was linked to shifts in C_org sources. The increase in the δ¹³C isotopic signature of sedimentary C_org (towards a higher seagrass contribution) at the Stone Town site since 1998 points to improved seagrass meadow conditions and C_org accumulation capacity of the meadow after the relocation of a major sewage outlet in the mid–1990s. In contrast, the decrease in the δ¹³C signatures of sedimentary C_org in the Mbweni meadow since the early 2010s was likely linked to increased C_org run-off of mangrove/terrestrial material following mangrove deforestation. This study exemplifies two different pathways by which land-based human activities can alter the carbon storage capacity of seagrass meadows (i.e. sewage waste management and mangrove deforestation) and showcases opportunities for management of vegetated coastal C_org sinks.