The object of this study is to assess the relevance of MRI water/fat separation to quantify fat and water in fish in a view of high throughput measurements. The major issue for this purpose is the spatial inhomogeneities of the signal. They are inherent to MRI and they may induce a position dependent bias in the quantification. We have combined water/fat separation methods from the literature and extended them in order to estimate these inhomogeneities. Experimental results show the efficiency of our method and validate the possibility to use MRI for water and fat quantification