The Rufiji River Delta (RRD) in Tanzania is an internationally important wetland. Subsistence mangrove rice farming (MRF) uses pesticides to combat crabs and herbicides to combat weeds. We undertook the first investigation of the dynamics of pesticide residues and hazard in farm soil, water, and sediment, during and following application. Twenty-one organochlorine and organophosphate insecticides, and the herbicide thiobencarb occurred at quantifiable concentrations. The residue profile indicated past use of organochlorine pesticides and current use of organophosphate pesticides (OPP). Residues of Sigma HCH4, Sigma DDT4, Sigma OPP5, and all residues combined (Sigma All(21)) in soils and sediments decreased significantly following application, but not for Sigma Cyclodienes(7). Sigma DDT4 and Sigma Cyclodienes(7) increased significantly in water following application, although this is likely related to legacy effects from upstream and not its use on MRFs. Sigma OPP5 made up 61% of Sigma All(21) in soils, 38% in sediments, and 45% in river water during application, dropping to 4.2%, 10%, and 19%, respectively, after application. Concentrations of compounds such as dieldrin, DDT, HCH, and OPPs exceeded various safety guidelines in all matrices. There were complicated dynamics of the residues between soils, sediments, and water, reflecting the complex interactions in a tidal riverine delta environment with the chronic presence of legacy pollutants and seasonal fluxes of current use pesticides. Multivariate analyses showed compound class specific differences in dynamics between matrixes and seasons. The predictions of pollutant concentrations and effects in highly biodiverse and productive tropical deltas with increasing human and extraction pressures, overlain with the spectre of climate change will be difficult. What seems certain though is that the stresses caused by chemicals will not lessen unless managed and calls for urgent interventions and further research. (c) 2020 Elsevier B.V. All rights reserved.