The protozoan parasites Cryptosporidium parvum, Cyclospora cayetanensis, and Toxoplasma gondii are major causes of waterborne and foodborne diseases worldwide. The assessment of their removal or inactivation during water treatment and food processing remains challenging, partly because research on these parasites is hindered by various economical, ethical, methodological, and biological constraints. To address public health concerns and gain new knowledge, researchers are increasingly seeking alternatives to the use of such pathogenic parasites. Over the past few decades, several non-pathogenic microorganisms and manufactured microparticles have been evaluated as potential surrogates of waterborne and foodborne protozoan parasites. Here, we review the surrogates that have been reported for C. parvum, C. cayetanensis, and T. gondii oocysts, and discuss their use and relevance to assess the transport, removal, and inactivation of these parasites in food and water matrices. Biological surrogates including non-human pathogenic Eimeria parasites, microorganisms found in water sources (anaerobic and aerobic spore-forming bacteria, algae), and non-biological surrogates (i.e. manufactured microparticles) have been identified. We emphasize that such surrogates have to be carefully selected and implemented depending on the parasite and the targeted application. Eimeria oocysts appear as promising surrogates to investigate in the future the pathogenic coccidian parasites C. cayetanensis and T. gondii that are the most challenging to work with.