Chwaka Bay is a predominantly rural setting part of Zanzibar Island, far away from any industrial establishments. Consequently, the area does not directly receive chemicals from industrial point sources. However, Chwaka Bay is located relatively close to the rice farms of Cheju, approximately 4 km west of the Bay (Fig. 1). Chwaka Bay is the drainage basin of the Cheju farms, but there are no direct surface water pathways between the rice fields and the Bay (Mmochi 2005). However, during the rain season, when the groundwater table is high, considerable surface runoff reaches the Bay (Tack 1997). There is also the possibility of groundwater intrusion due to the coralline structure of the underlying bedrock (Tack 1997). In Cheju, both fertilizers and pesticides for insect pests and weed control are used (Mmochi and Mberek 1998), making the Bay potentially vulnerable to input of agrochemicals.

The southern part of Chwaka Bay is fringed by a large mangrove forest, part of Jozani Park, which has the potential to trap both pesticides and nutrients from the Cheju runoff (Mohammed 1998; Kruitwagen et al. 2008). Chwaka Bay may also receive pesticides from fumigation and malaria control activities in the surrounding villages and tourist hotels, and nutrients from waste water and domestic animals. There is no sewerage system in the Chwaka Bay area and most villagers use pit latrines while some households do not even have toilets (uNEP/FAO/PAP 2000; see chap. 1).