Tropical deforestation contributes to atmospheric concentrations of greenhouse gases, linked to global climate change. In response, emerging markets for carbon emission offsets offer developing nations added incentives for rehabilitation and reforestation that increase terrestrial carbon storage. The Lower Tana River forests of northern Kenya are floodplain forest fragments supported by the river's groundwater and flooding. They provide numerous ecosystem services to local communities and habitat to endangered primates, but are vulnerable to altered hydrological conditions and clearance for cultivation. Forest carbon storage was sampled in the Tana River National Primate Reserve (TRNPR) and Tana Delta Irrigation Project (TDIP) and satellite imagery was used to assess land cover changes from 1992 to 2003. Riverine forest types had carbon densities ranging from 160 to 240 Mg C.ha⁻¹. Levee forests stored about 70 Mg C.ha⁻¹ more than forests further from the river, which may be transitioning to woodland savannah. A net loss of forest and woodland cover was seen in the satellite imagery and ongoing felling and clearance was seen in the field at both sites. Results indicated loss of carbon storage at both sampled sites, which may continue without efforts to increase landscape carbon stocks.