Seagrass meadows support high biodiversity and are important for invertebrate harvesting activities in developing countries. The aim of this study was to estimate the social and ecological effects of invertebrate harvesting, i.e. how this exploitation may affect/has affected seagrass variables (biomass, shoot density and canopy height), macrofaunal community structure, the use and importance of these resources for the livelihood of local people over time. A multi-disciplinary approach was used, including interviews with harvesters, observations of the number/activities of invertebrate harvesters, and a biological field study in Zanzibar, Tanzania. The study showed that women/children harvest invertebrates, and they prefer large seagrass patches, high to medium shoot density, and high seagrass cover. All interviewees said they had noticed a decline in seagrass distribution over the last decade, >20% considered it a large decline. Interviewees also reported decreased numbers of animals, but no change in the number of animal species over the last decade. The main reasons for the decline of seagrass and animals according to interviewees, are an increase in the number of harvesters, and a change in attitude, i.e. people being less careful about the intertidal zone and seagrasses. Invertebrate harvesting was found important for food security and provision of cash income. The current average catch weight was ca. 2 kg/collection day/person, and 3 kg and 5 kg, 5–10 and 30 years ago respectively according to interviewees. At present, the harvesting women earn ca 60–70% and ca 40% of what they would have if catches were the same sizes as they were 5–10 and 30 years ago respectively, according to our calculations. The field sampling within seagrass beds showed that an inaccessible/remote site had significantly higher invertebrate abundance and species richness/diversity than an exploited site (ANOVA). Multivariate statistics further revealed weak but significant differences for animal abundance and biomass between these sites. By combining findings from both interviews and field sampling this study shows that invertebrate harvesters can influence macrofaunal community structure in seagrass meadows, which in turn results in negative impacts on local harvesters’ economy and livelihood.