One of the less obvious, but most insidious, effects of the enormous changes in English agriculture over the past 50 years has been the contamination of groundwater—originally by nutrients, subsequently by pesticide residues, and most recently by the livestock parasite Cryptosporidium. The paper analyses scientific understanding of the factors determining the origin, transport and attenuation of these contaminants in groundwater systems. It focuses primarily on the British situation, but draws on experience from Europe and beyond as appropriate. Given the essentially diffuse character of the mainly agricultural activity generating the subsurface contaminant load, pollution control has (presented (and continues to present) a complex regulatory challenge in legal, technical, economic and social terms. The discussion explores this challenge, which yet again has become very topical at national and European policy levels.