The aim of this study was to investigate how long‐term Mancozeb application to banana plantations affects the occurrence of pollutants in drainage‐channel sediment and water under tropical conditions. We estimated the possible accumulation of Mancozeb's principal metabolite ethylenethiourea (ETU), as well as manganese (Mn) and zinc (Zn) as components in channel sediment and water. We took samples during the tropical‐rainfall season and the low‐rainfall season. For sediment samples, we determined the contents of ETU, Mn, and Zn. For water samples, we determined the concentration of ETU. Additionally, we took water samples from a runnel that is the receiving body of hydraulic flow from the system. In both seasons, ETU in the sediment was near the detection limit (0.01 mg kg–1) and did not show any accumulation. However, Mn in sediment at all sampling sites exceeded the threshold values for aquatic life of 630 mg kg–1 with values between 635 and 7256 mg kg–1. The Zn concentrations in sediment varied from 87 to 190 mg kg–1 and exceeded the threshold values for aquatic life of 98 mg kg–1 at several sites. Furthermore, we determined an accumulation of these heavy metals in the sediments of the banana‐planted zone in comparison with sediments in pasture reference sites. In contrast to the low concentration of ETU in sediment, its concentration in drainage and runnel water (5.9–13.8 μg L–1) exceeded the EU threshold value for drinking water (0.1 μg L–1) by up to nearly 140 times. However, the threshold value for aquatic life was not exceeded. We conclude that long‐term Mancozeb application does lead to a severe accumulation of Mn in sediments and of ETU in surface water. New strategies should be used to control black Sigatoka, including integrated methods of pest control so that long‐term negative effects on the environment can be avoided.