Urea-based multi-coated slow release fertilizer was produced using water hyacinth, humic substances, and chitosan, with water rich in natural organic matter as a solvent. Elemental analysis showed that the nitrogen content of the fertilizer (FERT) was around 20%. Swelling tests demonstrated the effectiveness of the water hyacinth crosslinker, which reduced the water permeability of the material. Leaching tests showed that FERT released a very low concentration of ammonium (0.82 mg L−1), compared to the amount released from urea (43.1 mg L−1). No nitrate leaching was observed for FERT, while urea leached 13.1 mg L−1 of nitrate. In water and soil, FERT showed maximum releases after 30 and 40 days, respectively, while urea reached maxima in just 2 and 5 days, respectively. The results demonstrated the promising ability of FERT to reduce nitrogen losses, as well as to minimize environmental impacts in the soil–plant-atmosphere system and to improve the efficiency of nitrogen fertilization. Graphic abstract