This study reports the status of pesticide pollution associated with rice farming in the hydromorphic valleys in Pemba. Analysis of surface waters, ground waters and soil revealed presence of ten types of pesticide residues belong to organochlorine pesticides (OCPs), organophosphate pesticides (OPPs) and herbicides. The residue composition indicated fingerprints of past use of OCPs coupled with current use OPPs and herbicides. There were no significant variations among the valleys but clear distinction of current use of OPPs in valleys under community management from past of OCPs in government managed valleys. The valleys showed significant variations of OPPs levels between the sampling periods while OCPs were quite stable with the exception HCHs. The spatial distribution was largely influenced by use pattern under existing governance of the valleys whereas temporal variations reflect the low persistence of OPPs and herbicides in tropical environment. Although the measured levels were in a lower side of the related studies but detection of OPPs in groundwater in some valleys call for the establishment of management and monitoring plans that will oversee use of pesticides in these valleys to safeguard the health of these fragile ecosystems.