The excessive use of fertilizers often left in abandoned plantations contributes greatly to eutrophication in local streams and lakes, and harms aquatic life after algal blooms deprive fish of oxygen. It has been theorized that destruction of 60% of coral reefs along the coasts of Costa Rica is partially from sediments from banana plantations. Another issue is the deforestation associated with expanding banana production. As monocultures rapidly deplete soil nutrients plantations expand to areas with rich soils and cut down forests, which also affects soil erosion and degradation, and increases frequency of flooding. The World Wildlife Fund (WWF) stated that banana production produced more waste than any other agricultural sector, mostly from discarded banana plants, bags used to cover the bananas, strings to tie them, and containers for transport.[87]

Voluntary sustainability standards such as Rainforest Alliance and Fairtrade are increasingly being used to address some of these issues. Bananas production certified by such sustainability standards experienced a 43% compound annual growth rate from 2008 to 2016, to represent 36% of banana exports.