Oceanographic and biogeochemical observations collected in Pemba Channel, a deep-water (800 m) channel separating Pemba Island from mainland Tanzania, during the South East monsoon indicate the presence of active upwelling along the western edge of Pemba Island. Surface salinity values, nutrient concentrations and the presence of coccolithophore species previously reported from the mid to lower euphotic zone all suggest up welling from at least 80–100 m depth. The surface waters of the channel were characterised with low NO3 − :PO4 3− (0.68:1) and NO3 − :Si (0.04:1) ratios far below the Brzezinski-Redfield ratio indicating the presence of N-limitation and the possibility that these waters may be susceptible to anthropogenic N inputs. Surface NO3 − concentrations averaged 0.09 ± 0.10 μmol L− 1 but increased to 0.5 μmol L− 1 in the centre of upwelling where coincidentally both integrated nutrient concentrations and surface POC/PON pools were approximately 2-fold higher than the channel average. Despite its significance for local productivity upwelling is tentatively estimated, via stoichio metric assumptions, to enhance local productivity by only 20%. The modest productivity response to upwelling may be explained by picoplankton (0.2–2 μm) dominance of the phytoplankton community with this size-class representing ~80% of total chlorophyll-a. Nevertheless, important spatial variability was identified in larger size fractions and supported by taxonomic analyses with indications that the distribution of Chaetoceros spp. alone may be particularly relevant for understanding the variability in larger (>20 μm) chlorophyll-a size fractions. The location of upwelling has previously been shown to host large concentrations of small pelagic fish thus management of this regionally important resource would benefit from additional investigation of the underlying physical mechanism driving upwelling and subsequently how trophic interactions and ecosystem productivity are influenced.funded through the UK Global Challenges Research Fund (GCRF) under NERC grant NE/P021050/1.