Acute diarrheal disease (ADD) caused by parasites and TB represent a significant public health burden worldwide and in Colombia, particularly affecting indigenous populations who are at high risk of contracting these diseases due to the social, environmental, and cultural conditions in which they live. Materials: Fifteen Wayuu indigenous communities in four areas of Manaure, in La Guajira, were subject to intervention; with prior informed consent, environmental samples and samples from individuals with clinical symptoms were collected. A total of 156 samples of human and animal feces, soil, and sediment from drinking water were analyzed for microscopic using the Kato–Katz and formalin–ether concentration techniques, 109 samples were analyzed by qPCR for the detection of helminths and 23 for metatranscriptomics targeting protozoan parasites and helminths. Additionally, 36 sputum samples from patients with respiratory symptoms were tested using Xpert/MTB Rif, and 37 milk samples were tested for M. bovis. Results: Among the samples tested for tuberculosis, a positivity rate of 8.3% was found, in all cases with sensitivity to rifampicin; M. bovis was not found in animal milk. Microscopic analysis of human samples revealed pathogenic parasites, the most common being Blastocystis spp. and the Entamoeba hystolitica/Entamoeba dispar complexeach with 38.8% (n=38), Giardia spp. with 19.4%, Hymenolepis nanaand Trichuris trichiura each with 5.1%. Commensal parasites were also identified as indicator of poor sanitary conditions. Co-infection with intestinal parasites was common in humans at 60.2%. In microscopic analysis of animals fecal samples, revealed a high incidence of Uncinaria spp. with 58.3%, amoebas 16.7% and Giardia 8.3%; this latter is also found in soil. Metatranscriptomics showed a high frequency of intestinal parasites in fecal samples (90.9%), with Blastocystis spp. being the most frequent (81.8%) with notable intra-species diversity, followed by Entamoeba histolytica (54.5%) and Giardia duodenalis (31.8%), and detected free-living amoebae in community water sources, highlighting potential health risks associated with exposure to untreated water in low-sanitation settings. Conclusions: The Wayuu communities studied show a significant burden of tuberculosis and intestinal parasitic infections, likely associated with poor sanitary conditions and environmental factors that facilitate their transmission. Although TB prevalence was moderate, with no evidence of rifampicin resistance or the circulation of M. bovis in milk, the high prevalence of intestinal parasites, including co-infections and their detection in humans, animals, and the environment suggest active transmission in the region. These findings highlight the need to implement comprehensive interventions in water, sanitation, and hygiene, along with surveillance and health education strategies with an intercultural approach, aimed at improving the conditions of these vulnerable populations.