This article analyses the endogenous choice of farmers to be organic or conventional in a groundwater evolutionary model when a tax on fertiliser on conventional farmers is implemented by a regulatory agency. The analysis of the model shows that the coexistence of both type of farmers only occurs when the decrease in productivity due to organic production is relatively low and the price premium for organic products is relatively high. However, even if conversion is welfare improving, our results show that this conversion may be done at the expense of the water resource with a lower water table. An application to the Western la Mancha aquifer (Spain) illustrates the main results.