The use of pesticides in Mozambique is increasing along with the development of agriculture in the country. Mangroves along the coastlines are ecologically important areas and vital nursing grounds for many aquatic species, several of which are of high economic value in Mozambique. Barred mudskipper (Periophthalmus argentilineatus), Jarbua fish (Terapon jarbua), Indian white prawn (Penaeus indicus) and the clam Meretrix meretrix were collected at three mangrove sites in the Maputo Bay area. This was complemented with samplings of the freshwater fish Mozambique tilapia (Oreochromis mossambicus), which was collected from three sampling sites along rivers in the surroundings of Maputo and from three sites along the Olifants and Limpopo River. Acetylcholinesterase (AChE) activity, which is an established biomarker for organophosphates and carbamate pesticides, was measured in brain and liver tissue in fish, and hepatopancreas tissue in prawn and clam. Butyrylcholinesterase (BChE) activity was also analyzed. Freshwater samples for pesticide analyses were collected in order to get an initial understanding of the classes and levels of pesticides present in aquatic systems in Mozambique. In addition to field samplings two 48-h exposure experiments were also conducted where the Indian white prawn and Barred mudskipper were exposed to malathion, and Mozambique tilapia exposed to malathion and diazinon. Field results show a significant decrease in AChE activity in fish from four of the sampling sites suggesting that pesticides present in water could be one stressor potentially affecting aquatic organisms negatively. The 48 h exposure experiment results showed a clear dose-response relationship of AChE activity in mudskipper and tilapia suggesting these species as suitable as sentinel species in environmental studies.