Algal genera such as Carteria, Chlamydomonas, Chlorogonium, Cryptomonas, Ceratium, Peridinium and Euglena are motile and may disrupt unit processes and cause water treatment problems. Algal species belonging to these motile algal genera are known to interfere with coagulation and flocculation unit processes which are the main processes for algal removal. These cells are well adapted, by means of their motile structures, morphological shapes and storage products, to remain in the supernatant (by swimming or floating) until it is carried over to sand filters, where cells may cause filter-clogging problems. When organic material is released from algal cells as a result of physical-chemical impacts on the cells, it may result in taste-and odour-related problems or the formation of harmful organic products such as trihalomethanes (THM). The aims of this study were to: (i) determine chlorine concentrations required to immobilise C. hirundinella cells; (ii) determine the removal efficiencies of pre-chlorination; (iii) investigate the integrity of C. hirundinella cells; and (iv) identify trihalomethanes that are formed. Source water samples enriched with C. hirundinella cells were exposed to a pre-determined chlorine concentration range (0.05-0.45 mg/L). This study found that the half-maximal inhibitory concentration (IC50-values) for chlorine < 0.20 mg/L is sufficient to render C. hirundinella cells immobile, while cells remain intact. Pre-chlorination did not have an impact on C. hirundinella removal when hydrated lime was used as a coagulant or coagulant aid. However, when organic polymer only was used as coagulant, removal efficiencies were improved by 20%. Chlorine by-products were measured, but posed no specific health risks to drinking water consumers due to the low concentration levels measured. Algal removal challenges that occur in water treatment plants when dosing organic polymers can be resolved by implementation of effective pre-chlorination strategies.