Pesticides are used worldwide with potential harmful effects on both fauna and flora. The Kibale National Park in Uganda, a site renowned for its biodiversity is surrounded by tea, banana and eucalyptus plantations as well as maize fields and small farms. We previously showed presence of pesticides with potential endocrine disruptive effects in the vicinity. To further investigate the water pollution linked to agricultural pressure in this protected area, we implemented a complementary monitoring strategy based on: analytical chemistry, effects based methods and the deployment of Polar Organic Chemical Integrative Samplers (POCIS). Chemical analysis of the POCIS extracts revealed the presence of 13 pesticides: carbofuran, DEET, 2.4-D amine, carbaryl, ametryn, isoproturon, metolachlor, terbutryn, dimethoate, imidacloprid, picaridin, thiamethoxam, carbendazim, with the first three being present in the largest quantities. Water samples collected at the POCIS sampling sites exhibited thyroid and estrogen axis disrupting activities in vivo, in addition to developmental and behaviour effects on Xenopus laevis tadpoles model. Based on our observations, for the health of local human and wildlife populations, further monitoring as well as actions to reduce agrochemical use should be considered in the Kibale National Park and in regions exposed to similar conditions.