[1] He is known for his research on ocean acidification, mercury pollution, the only known cadmium metalloenzyme, and the interactions between trace metals and microorganisms.

[7] The development of computational methods to quantify the reactions among the many chemical species in aquatic systems provided the means to study quantitatively the interactions between microbes and chemical elements and compounds present in natural waters, with a focus on essential metals that are required for the growth of phytoplankton.

[1][2][4][12][13] As a postdoctoral fellow in Environmental Engineering Sciences from 1971-1973, Morel collaborated with James (Jim) J. Morgan to produce the computer program REDEQL (where RED stands for "redox" and EQL stands for "equilibrium"), which computed complex chemical equilibria in natural waters and man-made chemical systems.

[1][14][7] Morel and Morgan's creation of REDEQL was supported by the United States Environmental Protection Agency and was widely adopted and built upon.

[14][7] In 2009, Morel chaired the Committee on the Development of an Integrated Science Strategy for Ocean Acidification Monitoring, Research, and Impacts Assessment.