© 2018 Elsevier Ltd There is an increasing demand for N-fertilizers and the manufacture of N-products worldwide. In Mexico, ammonia production is being promoted by the government, but this development is associated with several environmental impacts. This study examines the causes, effects and mitigation alternatives related to the installation and operation of an ammonia production plant adjacent to a coastal lagoon. A multiplicity of causes (and effects) was identified: water suction (elimination of plankton and larvae), effluent discharge (thermal contamination, salinization, and the effects of chlorine), and the conversion of wetlands (loss of habitat and nursery areas, biodiversity, fishery benefits, retention of contaminants, coastal stabilization, carbon storage and aesthetic value). At present, it is estimated that wetlands (9146 ha mangroves + 22,641 ha others) in the Ohuira-Topolobampo lagoon sustain the production of 3000 t live weight of seafood catches per year, implying that the conversion of 126 ha of wetlands could represent for fishermen a catch reduction of 11.9–41.3 t of shellfish per year and a decrease in the annual retention load of up 0.52 kg Cd, 41.0 kg Cu, 0.40 kg Hg, 280 kg Pb, 88.2 t P and 75.6 t N by wetland sediments. To mitigate the environmental effects associated with the installation and operation of the plant, the following is recommended: (i) afforestation of an equivalent area (126 ha), (ii) installation of an exclusion system for fauna to avoid the incidental capture of plankton and larvae, (iii) the use of cooling towers, and (iv) the selection of an appropriate discharge point for the effluent. A list of fauna and flora of the lagoon, as well as environmental services that could be compromised and affected by the operation of the ammonia production plant, is presented. This study is the first to analyze and document such effects and mitigation options related to land conversion and water management, providing useful information for decision makers.