The Belén District in Loreto Region, Peru, is known for its extensive riverfront areas, where many houses are built on stilts and float during the rainy season. We conducted fecal examinations on 997 schoolchildren (ages 4–14 years; 488 boys, 497 girls) across 4 schools in Belén using the Kato-Katz thick smear and formalin-ethyl acetate sedimentation techniques. The results revealed high rates of soilborne helminths and waterborne protozoan infections, with an overall parasite-positive rate of 79.7%. The primary helminth species were Ascaris lumbricoides (39.2%), Trichuris trichiura (33.2%), Hymenolepis nana (3.4%), hookworms (2.1%), and Enterobius vermicularis (1.5%). The main pathogenic protozoans were Giardia lamblia (20.9%) and Entamoeba histolytica/E. dispar (14.2%), along with Cryptosporidium-like coccidian (4.6%). Non-pathogenic protozoans included Entamoeba coli (31.5%), Endolimax nana (15.1%), and Blastocystis hominis (3.7%). The intensity of soilborne helminth infections was very high for A. lumbricoides (average eggs per gram of feces per child: 18,589), followed by T. trichiura (1,501) and hookworms (160). The prevalence of anemia, often associated with malnutrition, was moderate at 33.1% (298 anemic children among 901 examined). Mass deworming was initiated with albendazole 400 mg, 3 times a year, in conjunction with health education and environmental sanitation. Metronidazole was administered once at a dose of 200 mg 3 times daily for 10 days. A notable finding in this study was that soilborne and waterborne parasites are both highly prevalent among schoolchildren in the floating villages of the Belén District, Loreto Region. Sustained mass deworming is urgently needed and the WASH program is crucial.