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This study evaluated the seasonal and spatial variations in the presence of Giardia and Cryptosporidium in rural drinking water supply systems of different municipalities of Antioquia. The municipalities evaluated were Envigado, Caldas, Sabaneta, La Estrella, Itagüi, Bello, Barbosa, Copacabana, and Girardota, located in the department of Antioquia, Colombia. The experimentation was carried out over 9 sampling campaigns in the period between July 2019 and November 2020. This period encompassed the two seasons presented in Colombia: dry and wet. Each municipality included in this study has a conventional basic drinking water treatment system (DWTS) which includes sand trap, rapid filtration, and chlorination. The results showed good removal efficiencies of Cryptosporidium and Giardia in the DWTS evaluated. However, evaluation of other characteristics of water quality and of the water quality risk index for human consumption (IRCA) showed concerning water quality conditions in the rural drinking water systems supply. The prevailing risk levels of the drinking water are medium, high, or non-viable sanitary, which means the population is supplied with water that does not meet the minimum quality criteria established by Colombian regulations.