There is a lack of epidemiological information concerning intestinal parasitic infections, and especially in soil-transmitted helminths, occurring in some departments of Nicaragua. Up to now, this is the first study involving two nearby areas (Puerto Cabezas and Siuna municipalities) of the Región Autónoma Atlántico Norte (R.A.A.N.). One stool sample was analyzed by Kato-Katz, formaldehyde-ethyl acetate concentration method and modified Ziehl–Neelsen technique, and a simple questionnaire concerning demographic, sanitary and behavioral data was distributed among 735 children and evaluated. Overall prevalence of infection reached 97.0%, being the highest prevalences detected in all Nicaragua. The higher protozoan prevalence appears in Siuna (94.5%), a rural interior municipality, with a typical tropical monsoon climate, while the higher helminths rates were reached in Puerto Cabezas (92.8%), the urbanized coastal capital, with a typical tropical rainforest climate. No statistical differences were found with regard to sex. However, the 6–11-year age-group children presented the highest prevalences. Most T. trichiura infections (59.4%) were of light intensity, while 51.7% of Ascaris lumbricoides were of moderate intensity. Multivariable logistic regression analysis indicated that those who drink rainwater and walk barefoot were 2.9 and 2.5 times more likely to have helminth infections, respectively. Results from one geographical setting might not be applied to other nearby with different climatic conditions. The use of anthelmintic drugs only will not be sufficient to bring prevalence to low levels. It is necessary to design geographically more specific intervention, with communication and interaction between different disciplines (e.g. parasitology, biochemistry, molecular biology, epidemiology, public health, etc.) being imperative to reduce STH infection.